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   
jebl.evolution.trees   
 

Uses of ImportException in jebl.evolution.align
 

Methods in jebl.evolution.align that throw ImportException
static void BartonSternberg.main(java.lang.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
          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
 boolean NewickImporter.hasTree()
           
 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.
 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.
 java.util.List<Alignment> NexusImporter.importAlignments()
          Import all alignments in the input from the current position.
 java.util.List<Alignment> AlignmentImporter.importAlignments()
          importAlignment.
 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.
 java.util.List<DistanceMatrix> DistanceMatrixImporter.importDistanceMatrices()
          importDistances.
 Tree NewickImporter.importNextTree()
           
 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.
 java.util.List<Sequence> FastaImporter.importSequences()
           
 java.util.List<Sequence> NexusImporter.importSequences()
          Import all sequences in the input from the current position
 java.util.List<Sequence> SequenceImporter.importSequences()
          importSequences.
 java.util.List<Sequence> PhylipSequentialImporter.importSequences()
          importSequences.
 void ImmediateSequenceImporter.importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener)
           
 void FastaImporter.importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener)
           
 java.util.List<Tree> NewickImporter.importTrees()
           
 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<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.
 

Uses of ImportException in jebl.evolution.trees
 

Methods in jebl.evolution.trees that throw ImportException
 void CalculateSplitRates.loadTrees(int maxTrees, int burnIn)
           
 



http://code.google.com/p/jebl2/