Uses of Class
jebl.evolution.io.ImportException
Packages that use ImportException
Package
Description
Provides classes and interfaces for pairwise alignment of two sequences.
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Uses of ImportException in jebl.evolution.align
Methods in jebl.evolution.align that throw ImportException -
Uses of ImportException in jebl.evolution.io
Subclasses of ImportException in jebl.evolution.ioModifier and TypeClassDescriptionstatic class
static class
static class
static class
static class
static class
static class
static class
static class
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 ImportExceptionModifier and TypeMethodDescriptionboolean
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
return whether another tree is available.trees = new ArrayList (); while (hasTree()) { trees.add(importNextTree()); } AlignmentImporter.importAlignments()
importAlignment.NexusImporter.importAlignments()
Import all alignments in the input from the current position.DistanceMatrixImporter.importDistanceMatrices()
importDistances.NexusImporter.importDistanceMatrices()
Import all distance matrices from all DISTANCES blocks in the input form the current position.TabDelimitedImporter.importDistanceMatrices()
importDistances.NewickImporter.importNextTree()
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.TreeImporter.importNextTree()
Import a single treeFastaImporter.importSequences()
void
FastaImporter.importSequences
(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener) void
ImmediateSequenceImporter.importSequences
(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener) NexusImporter.importSequences()
Import all sequences in the input from the current positionPhylipSequentialImporter.importSequences()
importSequences.SequenceImporter.importSequences()
importSequences.NewickImporter.importTrees()
NexusImporter.importTrees()
Import all trees in the file from the current position.TreeImporter.importTrees()
Import all the treesNexusImporter.parseCharactersBlock
(List<Taxon> taxonList) Parse the next 'CHARACTERS' block encountered in the input.NexusImporter.parseDataBlock
(List<Taxon> taxonList) Parse the next 'DATA' block encountered in the input.NexusImporter.parseDistancesBlock
(List<Taxon> taxonList) Parse the next 'DISTANCES' block encountered in the input.NexusImporter.parseTaxaBlock()
Parse the next 'TAXA' block encountered in the input.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