Uses of Class
jebl.evolution.io.ImportException

Packages that use ImportException

jebl.evolution.align	Provides classes and interfaces for pairwise alignment of two sequences.
jebl.evolution.io

Uses of ImportException in jebl.evolution.align

Methods in jebl.evolution.align that throw ImportException

static void

BartonSternberg.main(String[] arguments)

Uses of ImportException in jebl.evolution.io

Subclasses of ImportException in jebl.evolution.io

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

Methods in jebl.evolution.io that throw ImportException

boolean	NewickImporter.hasTree()
boolean	NexusImporter.hasTree() return whether another tree is available.
boolean	TreeImporter.hasTree() This can be used to read one tree at a time in a loop: List trees = new ArrayList(); while (hasTree()) { trees.add(importNextTree()); } return whether another tree is available.
List<Alignment>	AlignmentImporter.importAlignments() importAlignment.
List<Alignment>	NexusImporter.importAlignments() importAlignment.
List<DistanceMatrix>	DistanceMatrixImporter.importDistanceMatrices() importDistances.
List<DistanceMatrix>	NexusImporter.importDistanceMatrices() importDistances.
List<DistanceMatrix>	TabDelimitedImporter.importDistanceMatrices() importDistances.
Tree	NewickImporter.importNextTree()
Tree	NexusImporter.importNextTree() import the next tree.
Tree	TreeImporter.importNextTree() Import a single tree
List<Sequence>	FastaImporter.importSequences()
List<Sequence>	NexusImporter.importSequences() importSequences.
List<Sequence>	PhylipSequentialImporter.importSequences() importSequences.
List<Sequence>	SequenceImporter.importSequences() importSequences.
void	FastaImporter.importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener)
void	ImmediateSequenceImporter.importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener)
List<Tree>	NewickImporter.importTrees()
List<Tree>	NexusImporter.importTrees()
List<Tree>	TreeImporter.importTrees() Import all the trees
List<Sequence>	NexusImporter.parseCharactersBlock(List<Taxon> taxonList) Parses a 'CHARACTERS' block.
List<Sequence>	NexusImporter.parseDataBlock(List<Taxon> taxonList) Parses a 'DATA' block.
DistanceMatrix	NexusImporter.parseDistancesBlock(List<Taxon> taxonList)
List<Taxon>	NexusImporter.parseTaxaBlock() Parses a 'TAXA' block.
List<Tree>	NexusImporter.parseTreesBlock(List<Taxon> taxonList) Parses a 'TREES' block.
double	ImportHelper.readDouble() Attempts to read and parse a double delimited by whitespace.
double	ImportHelper.readDouble(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(String delimiters) Attempts to read and parse an integer delimited by whitespace or by any character in delimiters.
void	ImportHelper.readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence)
void	ImportHelper.readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence, ProgressListener progress) Reads sequence, skipping over any comments and filtering using sequenceType.
void	ImportHelper.readSequenceLine(StringBuffer sequence, SequenceType sequenceType, String delimiters, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence) Reads a line of sequence, skipping over any comments and filtering using sequenceType.
boolean	NexusImporter.startReadingTrees()