public class FASTAEventReader extends AbstractTextEventReader<TextReaderStreamDataProvider<FASTAEventReader>> implements FASTAConstants
This reader supports comments in lines following the name definition line. Additionally, indices preceding lines containing sequence data are allowed but are ignored by this reader.
Example:
>Sequence 1 ;Some comment ;Another comment 0 ACGT 5 TAGC 10 TTAGT >Sequence 2 ACGT-ACC-TAGT
This reader does not process the sequence names according to any conventions. The full string following '>'
will be returned in each SequenceTokensEvent
and can be parsed later on by the application.
lineConsumed
COMMENT_START_CHAR, DEFAULT_LINE_LENGTH, FASTA_FORMAT_NAME, NAME_START_CHAR
ATTRIBUTE_STRING_KEY, ATTRIBUTES_NAMESPACE_FOLDER, DATA_TYPE_NAMESPACE_FOLDER, DATA_TYPE_SIMPLE_VALUE_LIST, DEFAULT_CHAR_SET_ID_PREFIX, DEFAULT_CHARACTER_DEFINITION_ID_PREFIX, DEFAULT_EDGE_ID_PREFIX, DEFAULT_GENERAL_ID_PREFIX, DEFAULT_MATRIX_ID_PREFIX, DEFAULT_MAX_COMMENT_LENGTH, DEFAULT_MAX_TOKENS_TO_READ, DEFAULT_META_ID_PREFIX, DEFAULT_NETWORK_ID_PREFIX, DEFAULT_NODE_EDGE_SET_ID_PREFIX, DEFAULT_NODE_ID_PREFIX, DEFAULT_OTU_ID_PREFIX, DEFAULT_OTU_LIST_ID_PREFIX, DEFAULT_OTU_SET_ID_PREFIX, DEFAULT_SEQUENCE_ID_PREFIX, DEFAULT_SEQUENCE_SET_ID_PREFIX, DEFAULT_TOKEN_DEFINITION_ID_PREFIX, DEFAULT_TOKEN_SET_ID_PREFIX, DEFAULT_TREE_ID_PREFIX, DEFAULT_TREE_NETWORK_GROUP_ID_PREFIX, DEFAULT_TREE_NETWORK_SET_ID_PREFIX, JPHYLOIO_ATTRIBUTES_NAMESPACE, JPHYLOIO_ATTRIBUTES_PREFIX, JPHYLOIO_DATA_TYPE_NAMESPACE, JPHYLOIO_DATA_TYPE_PREFIX, JPHYLOIO_FORMATS_NAMESPACE_PREFIX, JPHYLOIO_GENERAL_NAMESPACE, JPHYLOIO_NAMESPACE_PREFIX, JPHYLOIO_PREDICATE_NAMESPACE, JPHYLOIO_PREDICATE_PREFIX, PREDICATE_CHARACTER_COUNT, PREDICATE_EDGE_LENGTH, PREDICATE_EDGE_SOURCE_NODE, PREDICATE_EDGE_TARGET_NODE, PREDICATE_HAS_CUSTOM_XML, PREDICATE_HAS_LITERAL_METADATA, PREDICATE_HAS_RESOURCE_METADATA, PREDICATE_IS_CROSSLINK, PREDICATE_NAMESPACE_FOLDER, PREDICATE_PART_SEPERATOR, PREDICATE_SEQUENCE_COUNT, RESERVED_ID_PREFIX
Constructor and Description |
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FASTAEventReader(java.io.BufferedReader reader,
ReadWriteParameterMap parameters)
Creates a new instance of this class.
|
FASTAEventReader(java.io.File file,
ReadWriteParameterMap parameters)
Creates a new instance of this class.
|
FASTAEventReader(java.io.InputStream stream,
ReadWriteParameterMap parameters)
Creates a new instance of this class.
|
FASTAEventReader(java.io.Reader reader,
ReadWriteParameterMap parameters)
Creates a new instance of this class.
|
Modifier and Type | Method and Description |
---|---|
java.lang.String |
getFormatID()
Returns a string ID uniquely identifying the target format of this instance.
|
protected void |
readNextEvent()
Method to be implemented be inherited classes that adds at least one additional event (determined from
the underlying data source) to the event queue.
|
close, consumeWhiteSpaceAndComments, createStreamDataProvider, createTokenList, getReader, readCharacters, readCharacters, readComment, readKeyValueInformation, readToken
addEventListener, fireEvent, getCurrentEventCollection, getIDManager, getLastNonCommentEvent, getParameters, getParentInformation, getPreviousEvent, getSequenceTokensEventManager, getStreamDataProvider, getUpcomingEvents, hasNextEvent, hasSpecialEventCollection, isBeforeFirstAccess, next, nextOfType, peek, removeEventListener, resetCurrentEventCollection, setCurrentEventCollection
public FASTAEventReader(java.io.BufferedReader reader, ReadWriteParameterMap parameters) throws java.io.IOException
reader
- the reader providing the FASTA data to be readparameters
- the parameter map for this reader instancejava.io.IOException
- if an I/O exception occurs while parsing the first eventpublic FASTAEventReader(java.io.File file, ReadWriteParameterMap parameters) throws java.io.IOException
file
- the FASTA file to be readparameters
- the parameter map for this reader instancejava.io.IOException
- if an I/O exception occurs while parsing the first eventpublic FASTAEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters) throws java.io.IOException
stream
- the stream providing the FASTA data to be readparameters
- the parameter map for this reader instancejava.io.IOException
- if an I/O exception occurs while parsing the first eventpublic FASTAEventReader(java.io.Reader reader, ReadWriteParameterMap parameters) throws java.io.IOException
reader
- the reader providing the FASTA data to be readparameters
- the parameter map for this reader instancejava.io.IOException
- if an I/O exception occurs while parsing the first eventpublic java.lang.String getFormatID()
JPhyloIOFormatSpecificObject
JPhyloIOReaderWriterFactory.getFormatInfo(String)
.
Third party developers that create readers or writers for additional formats must make sure to use a globally unique
format ID. It is strongly recommended to use owned reverse domain names for this (e.g.
org.example.additionalformat
).
getFormatID
in interface JPhyloIOFormatSpecificObject
JPhyloIOReaderWriterFactory.getFormatInfo(String)
protected void readNextEvent() throws java.io.IOException
AbstractEventReader
readNextEvent
in class AbstractEventReader<TextReaderStreamDataProvider<FASTAEventReader>>
java.io.IOException