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.
lineConsumedCOMMENT_START_CHAR, DEFAULT_LINE_LENGTH, FASTA_FORMAT_NAME, NAME_START_CHARATTRIBUTE_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 |
|---|
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, readTokenaddEventListener, fireEvent, getCurrentEventCollection, getIDManager, getLastNonCommentEvent, getParameters, getParentInformation, getPreviousEvent, getSequenceTokensEventManager, getStreamDataProvider, getUpcomingEvents, hasNextEvent, hasSpecialEventCollection, isBeforeFirstAccess, next, nextOfType, peek, removeEventListener, resetCurrentEventCollection, setCurrentEventCollectionpublic 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()
JPhyloIOFormatSpecificObjectJPhyloIOReaderWriterFactory.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 JPhyloIOFormatSpecificObjectJPhyloIOReaderWriterFactory.getFormatInfo(String)protected void readNextEvent() throws java.io.IOException
AbstractEventReaderreadNextEvent in class AbstractEventReader<TextReaderStreamDataProvider<FASTAEventReader>>java.io.IOException