# Uses of Class
jebl.evolution.io.ImportException

Packages that use ImportException
Package
Description
jebl.evolution.align
Provides classes and interfaces for pairwise alignment of two sequences.
jebl.evolution.io
jebl.evolution.trees

## Uses of ImportException in jebl.evolution.align

Methods in jebl.evolution.align that throw ImportException
Modifier and Type
Method
Description
`static void`
BartonSternberg.`main(String[] arguments)`

## Uses of ImportException in jebl.evolution.io

Subclasses of ImportException in jebl.evolution.io
Modifier and Type
Class
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.
Methods in jebl.evolution.io that throw ImportException
Modifier and Type
Method
Description
`boolean`
NewickImporter.`hasTree()`
`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`
TreeImporter.`hasTree()`
This can be used to read one tree at a time in a loop: `List<Tree> trees = new ArrayList<Tree>(); while (hasTree()) { trees.add(importNextTree()); }` return whether another tree is available.
`List<Alignment>`
AlignmentImporter.`importAlignments()`
importAlignment.
`List<Alignment>`
NexusImporter.`importAlignments()`
Import all alignments in the input from the current position.
`List<DistanceMatrix>`
DistanceMatrixImporter.`importDistanceMatrices()`
importDistances.
`List<DistanceMatrix>`
NexusImporter.`importDistanceMatrices()`
Import all distance matrices from all DISTANCES blocks in the input form the current position.
`List<DistanceMatrix>`
TabDelimitedImporter.`importDistanceMatrices()`
importDistances.
`Tree`
NewickImporter.`importNextTree()`
`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`
TreeImporter.`importNextTree()`
Import a single tree
`final List<Sequence>`
FastaImporter.`importSequences()`
`void`
FastaImporter.`importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener)`
`void`
ImmediateSequenceImporter.`importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener)`
`List<Sequence>`
NexusImporter.`importSequences()`
Import all sequences in the input from the current position
`List<Sequence>`
PhylipSequentialImporter.`importSequences()`
importSequences.
`List<Sequence>`
SequenceImporter.`importSequences()`
importSequences.
`List<Tree>`
NewickImporter.`importTrees()`
`List<Tree>`
NexusImporter.`importTrees()`
Import all trees in the file from the current position.
`List<Tree>`
TreeImporter.`importTrees()`
Import all the trees
`List<Sequence>`
NexusImporter.`parseCharactersBlock(List<Taxon> taxonList)`
Parse the next 'CHARACTERS' block encountered in the input.
`List<Sequence>`
NexusImporter.`parseDataBlock(List<Taxon> taxonList)`
Parse the next 'DATA' block encountered in the input.
`DistanceMatrix`
NexusImporter.`parseDistancesBlock(List<Taxon> taxonList)`
Parse the next 'DISTANCES' block encountered in the input.
`List<Taxon>`
NexusImporter.`parseTaxaBlock()`
Parse the next 'TAXA' block encountered in the input.
`List<Tree>`
NexusImporter.`parseTreesBlock(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(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, boolean stopAtDoubleNewLine)`
`void`
ImportHelper.`readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence, ProgressListener progress)`
`void`
ImportHelper.`readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence, ProgressListener progress, boolean stopAtDoubleNewLine)`
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()`
Read nexus blocks until the next TREES block (or the end of the input) is encountered.

## Uses of ImportException in jebl.evolution.trees

Methods in jebl.evolution.trees that throw ImportException
Modifier and Type
Method
Description
`void`
CalculateSplitRates.`loadTrees(int maxTrees, int burnIn)`