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 classstatic classstatic classstatic classstatic classstatic classstatic classstatic classstatic classThrown 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 TypeMethodDescriptionbooleanNewickImporter.hasTree()booleanNexusImporter.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.booleanTreeImporter.hasTree()This can be used to read one tree at a time in a loop:Listreturn 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()voidFastaImporter.importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener) voidImmediateSequenceImporter.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.doubleImportHelper.readDouble()Attempts to read and parse a double delimited by whitespace.doubleImportHelper.readDouble(String delimiters) Attempts to read and parse a double delimited by whitespace or by any character in delimiters.intImportHelper.readInteger()Attempts to read and parse an integer delimited by whitespace.intImportHelper.readInteger(String delimiters) Attempts to read and parse an integer delimited by whitespace or by any character in delimiters.voidImportHelper.readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence) voidImportHelper.readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence, boolean stopAtDoubleNewLine) voidImportHelper.readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence, ProgressListener progress) voidImportHelper.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.voidImportHelper.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.booleanNexusImporter.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