Package | Description |
---|---|
jebl.evolution.alignments | |
jebl.evolution.io | |
jebl.evolution.sequences | |
jebl.evolution.substmodel |
Modifier and Type | Method | Description |
---|---|---|
SequenceType |
BasicAlignment.getSequenceType() |
|
SequenceType |
ConsensusSequence.getSequenceType() |
|
SequenceType |
Pattern.getSequenceType() |
|
SequenceType |
Patterns.getSequenceType() |
|
SequenceType |
ResampledAlignment.getSequenceType() |
Modifier and Type | Method | Description |
---|---|---|
void |
ImportHelper.readSequence(java.lang.StringBuilder sequence,
SequenceType sequenceType,
java.lang.String delimiters,
int maxSites,
java.lang.String gapCharacters,
java.lang.String missingCharacters,
java.lang.String matchCharacters,
java.lang.String matchSequence) |
|
void |
ImportHelper.readSequence(java.lang.StringBuilder sequence,
SequenceType sequenceType,
java.lang.String delimiters,
int maxSites,
java.lang.String gapCharacters,
java.lang.String missingCharacters,
java.lang.String matchCharacters,
java.lang.String matchSequence,
boolean stopAtDoubleNewLine) |
|
void |
ImportHelper.readSequence(java.lang.StringBuilder sequence,
SequenceType sequenceType,
java.lang.String delimiters,
int maxSites,
java.lang.String gapCharacters,
java.lang.String missingCharacters,
java.lang.String matchCharacters,
java.lang.String matchSequence,
ProgressListener progress) |
|
void |
ImportHelper.readSequence(java.lang.StringBuilder sequence,
SequenceType sequenceType,
java.lang.String delimiters,
int maxSites,
java.lang.String gapCharacters,
java.lang.String missingCharacters,
java.lang.String matchCharacters,
java.lang.String matchSequence,
ProgressListener progress,
boolean stopAtDoubleNewLine) |
Reads sequence, skipping over any comments and filtering using sequenceType.
|
void |
ImportHelper.readSequenceLine(java.lang.StringBuffer sequence,
SequenceType sequenceType,
java.lang.String delimiters,
java.lang.String gapCharacters,
java.lang.String missingCharacters,
java.lang.String matchCharacters,
java.lang.String matchSequence) |
Reads a line of sequence, skipping over any comments and filtering using sequenceType.
|
Constructor | Description |
---|---|
FastaImporter(java.io.File file,
SequenceType sequenceType) |
Use this constructor if you are reading from a file.
|
FastaImporter(java.io.Reader reader,
SequenceType sequenceType) |
This constuctor takes a reader.
|
PhylipSequentialImporter(java.io.Reader reader,
SequenceType sequenceType,
int maxNameLength) |
Constructor
|
Modifier and Type | Field | Description |
---|---|---|
static SequenceType |
SequenceType.AMINO_ACID |
|
static SequenceType |
SequenceType.CODON |
|
static SequenceType |
SequenceType.NUCLEOTIDE |
Modifier and Type | Method | Description |
---|---|---|
SequenceType |
BasicSequence.getSequenceType() |
|
SequenceType |
CanonicalSequence.getSequenceType() |
|
SequenceType |
CodonSequence.getSequenceType() |
|
SequenceType |
FilteredSequence.getSequenceType() |
|
SequenceType |
Sequence.getSequenceType() |
|
SequenceType |
TranslatedSequence.getSequenceType() |
|
static SequenceType |
Utils.guessSequenceType(java.lang.CharSequence seq) |
Guess type of sequence from contents.
|
Modifier and Type | Method | Description |
---|---|---|
static State[] |
Utils.cleanSequence(java.lang.CharSequence seq,
SequenceType type) |
Produce a clean sequence filtered of spaces and digits.
|
static java.lang.String |
SequenceType.Utils.getAlphabet(SequenceType sequenceType) |
Constructor | Description |
---|---|
BasicSequence(SequenceType sequenceType,
Taxon taxon,
java.lang.CharSequence sequenceString) |
Creates a sequence with a name corresponding to the taxon name.
|
BasicSequence(SequenceType sequenceType,
Taxon taxon,
State[] states) |
Creates a sequence with a name corresponding to the taxon name
|
CanonicalSequence(SequenceType sequenceType,
Taxon taxon,
java.lang.CharSequence sequenceString) |
Creates a sequence with a name corresponding to the taxon name.
|
CanonicalSequence(SequenceType sequenceType,
Taxon taxon,
State[] states) |
Creates a sequence with a name corresponding to the taxon name
|
Modifier and Type | Method | Description |
---|---|---|
SequenceType |
AbstractRateMatrix.getSequenceType() |
|
SequenceType |
RateMatrix.getSequenceType() |
Get the data type of this rate matrix
|
http://code.google.com/p/jebl2/