Package | Description |
---|---|
jebl.evolution.align |
Provides classes and interfaces for pairwise alignment of two sequences.
|
jebl.evolution.io | |
jebl.evolution.trees |
Modifier and Type | Method and Description |
---|---|
static void |
BartonSternberg.main(java.lang.String[] arguments) |
Modifier and Type | Class and Description |
---|---|
static class |
ImportException.BadFormatException |
static class |
ImportException.DuplicateFieldException |
static class |
ImportException.DuplicateTaxaException |
static class |
ImportException.MissingFieldException |
static class |
ImportException.ShortSequenceException |
static class |
ImportException.TooFewTaxaException |
static class |
ImportException.UnknownTaxonException |
static class |
ImportException.UnparsableDataException |
static class |
NexusImporter.MissingBlockException
Thrown when a block is missing that is required for importing a particular type of data from the nexus input.
|
Modifier and Type | Method and Description |
---|---|
boolean |
TreeImporter.hasTree()
This can be used to read one tree at a time in a loop:
List
return whether another tree is available. |
boolean |
NexusImporter.hasTree()
If not currently reading a TREES block then read ahead to the next TREES block, parsing TRANSLATE and TAXA blocks
in the process if necessary.
|
boolean |
NewickImporter.hasTree() |
java.util.List<Alignment> |
AlignmentImporter.importAlignments()
importAlignment.
|
java.util.List<Alignment> |
NexusImporter.importAlignments()
Import all alignments in the input from the current position.
|
java.util.List<DistanceMatrix> |
DistanceMatrixImporter.importDistanceMatrices()
importDistances.
|
java.util.List<DistanceMatrix> |
NexusImporter.importDistanceMatrices()
Import all distance matrices from all DISTANCES blocks in the input form the current position.
|
java.util.List<DistanceMatrix> |
TabDelimitedImporter.importDistanceMatrices()
importDistances.
|
Tree |
TreeImporter.importNextTree()
Import a single tree
|
Tree |
NexusImporter.importNextTree()
If not currently reading a TREES block then read ahead to the next TREES block, parsing TRANSLATE and TAXA blocks
in the process if necessary.
|
Tree |
NewickImporter.importNextTree() |
java.util.List<Sequence> |
SequenceImporter.importSequences()
importSequences.
|
java.util.List<Sequence> |
PhylipSequentialImporter.importSequences()
importSequences.
|
java.util.List<Sequence> |
FastaImporter.importSequences() |
java.util.List<Sequence> |
NexusImporter.importSequences()
Import all sequences in the input from the current position
|
void |
FastaImporter.importSequences(ImmediateSequenceImporter.Callback callback,
ProgressListener progressListener) |
void |
ImmediateSequenceImporter.importSequences(ImmediateSequenceImporter.Callback callback,
ProgressListener progressListener) |
java.util.List<Tree> |
TreeImporter.importTrees()
Import all the trees
|
java.util.List<Tree> |
NexusImporter.importTrees()
Import all trees in the file from the current position.
|
java.util.List<Tree> |
NewickImporter.importTrees() |
java.util.List<Sequence> |
NexusImporter.parseCharactersBlock(java.util.List<Taxon> taxonList)
Parse the next 'CHARACTERS' block encountered in the input.
|
java.util.List<Sequence> |
NexusImporter.parseDataBlock(java.util.List<Taxon> taxonList)
Parse the next 'DATA' block encountered in the input.
|
DistanceMatrix |
NexusImporter.parseDistancesBlock(java.util.List<Taxon> taxonList)
Parse the next 'DISTANCES' block encountered in the input.
|
java.util.List<Taxon> |
NexusImporter.parseTaxaBlock()
Parse the next 'TAXA' block encountered in the input.
|
java.util.List<Tree> |
NexusImporter.parseTreesBlock(java.util.List<Taxon> taxonList)
Parse the next 'TREES' block encountered in the input.
|
double |
ImportHelper.readDouble()
Attempts to read and parse a double delimited by whitespace.
|
double |
ImportHelper.readDouble(java.lang.String delimiters)
Attempts to read and parse a double delimited by whitespace or by
any character in delimiters.
|
int |
ImportHelper.readInteger()
Attempts to read and parse an integer delimited by whitespace.
|
int |
ImportHelper.readInteger(java.lang.String delimiters)
Attempts to read and parse an integer delimited by whitespace or by
any character in delimiters.
|
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.
|
boolean |
NexusImporter.startReadingTrees()
Read nexus blocks until the next TREES block (or the end of the input) is encountered.
|
Modifier and Type | Method and Description |
---|---|
void |
CalculateSplitRates.loadTrees(int maxTrees,
int burnIn) |
http://code.google.com/p/jebl2/