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Packages that use ImportException | |
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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 |
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Methods in jebl.evolution.align that throw ImportException | |
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static void |
BartonSternberg.main(java.lang.String[] arguments)
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Uses of ImportException in jebl.evolution.io |
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Subclasses of ImportException in jebl.evolution.io | |
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static class |
ImportException.BadFormatException
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static class |
ImportException.DuplicateFieldException
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static class |
ImportException.DuplicateTaxaException
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static class |
ImportException.MissingFieldException
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static class |
ImportException.ShortSequenceException
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static class |
ImportException.TooFewTaxaException
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static class |
ImportException.UnknownTaxonException
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static class |
ImportException.UnparsableDataException
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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 | |
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boolean |
NewickImporter.hasTree()
|
boolean |
TreeImporter.hasTree()
This can be used to read one tree at a time in a loop:
List
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()
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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)
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java.util.List<Tree> |
NewickImporter.importTrees()
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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 |
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Methods in jebl.evolution.trees that throw ImportException | |
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void |
CalculateSplitRates.loadTrees(int maxTrees,
int burnIn)
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