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 trees = new ArrayList();
while (hasTree()) {
trees.add(importNextTree());
}
return whether another tree is available.
|
java.util.List<Alignment> |
AlignmentImporter.importAlignments() |
importAlignment.
|
java.util.List<Alignment> |
NexusImporter.importAlignments() |
Import all alignments in the input from the current position.
|
java.util.List<DistanceMatrix> |
DistanceMatrixImporter.importDistanceMatrices() |
importDistances.
|
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.
|
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
|
java.util.List<Sequence> |
FastaImporter.importSequences() |
|
void |
FastaImporter.importSequences(ImmediateSequenceImporter.Callback callback,
ProgressListener progressListener) |
|
void |
ImmediateSequenceImporter.importSequences(ImmediateSequenceImporter.Callback callback,
ProgressListener progressListener) |
|
java.util.List<Sequence> |
NexusImporter.importSequences() |
Import all sequences in the input from the current position
|
java.util.List<Sequence> |
PhylipSequentialImporter.importSequences() |
importSequences.
|
java.util.List<Sequence> |
SequenceImporter.importSequences() |
importSequences.
|
java.util.List<Tree> |
NewickImporter.importTrees() |
|
java.util.List<Tree> |
NexusImporter.importTrees() |
Import all trees in the file from the current position.
|
java.util.List<Tree> |
TreeImporter.importTrees() |
Import all the trees
|
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.
|