Package htsjdk.beta.codecs.hapref.fasta
Class FASTADecoderV1_0
java.lang.Object
htsjdk.beta.codecs.hapref.fasta.FASTADecoderV1_0
- All Implemented Interfaces:
HaploidReferenceDecoder
,HtsDecoder<SAMSequenceDictionary,
,ReferenceSequence> HtsQuery<ReferenceSequence>
,Closeable
,AutoCloseable
,Iterable<ReferenceSequence>
The v1.0 FASTA decoder.
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
close()
Close any resources associated with this decoder.Get a user-friendly display name for this decoder.final String
Get the name of the file format supported by this decoder.The format name defines the underlying format handled by this decoder, and also corresponds to the format of the primary bundle resource that is required when decoding (seeBundleResourceType
andBundleResource.getFileFormat()
).Get the file header for this decoder.Get the version of the file format supported by this decoder.boolean
hasIndex()
Return true if the underlying resource has an index.boolean
Gte true if the underlying resource is queryable.iterator()
Get an iterator of all records in the underlying resource.Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface htsjdk.beta.plugin.interval.HtsQuery
query, query, query, query, queryContained, queryContained, queryContained, queryOverlapping, queryOverlapping, queryOverlapping, queryStart
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Field Details
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inputBundle
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Constructor Details
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FASTADecoderV1_0
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Method Details
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getDisplayName
Description copied from interface:HtsDecoder
Get a user-friendly display name for this decoder.- Specified by:
getDisplayName
in interfaceHtsDecoder<SAMSequenceDictionary,
ReferenceSequence> - Returns:
- a user-friendly display name for this decoder for use in error and warning messages
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getFileFormat
Description copied from interface:HtsDecoder
Get the name of the file format supported by this decoder.The format name defines the underlying format handled by this decoder, and also corresponds to the format of the primary bundle resource that is required when decoding (seeBundleResourceType
andBundleResource.getFileFormat()
).- Specified by:
getFileFormat
in interfaceHtsDecoder<SAMSequenceDictionary,
ReferenceSequence> - Returns:
- the name of the underlying file format handled by this decoder
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getHeader
Description copied from interface:HtsDecoder
Get the file header for this decoder.- Specified by:
getHeader
in interfaceHtsDecoder<SAMSequenceDictionary,
ReferenceSequence> - Returns:
- the file header for this decoder, of type
H
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getVersion
Description copied from interface:HtsDecoder
Get the version of the file format supported by this decoder.- Specified by:
getVersion
in interfaceHtsDecoder<SAMSequenceDictionary,
ReferenceSequence>
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iterator
Description copied from interface:HtsQuery
Get an iterator of all records in the underlying resource.- Specified by:
iterator
in interfaceHtsQuery<ReferenceSequence>
- Specified by:
iterator
in interfaceIterable<ReferenceSequence>
- Returns:
- an iterator of all records in the underlying resource
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isQueryable
public boolean isQueryable()Description copied from interface:HtsQuery
Gte true if the underlying resource is queryable.- Specified by:
isQueryable
in interfaceHtsQuery<ReferenceSequence>
- Returns:
- true if the underlying resource is queryable. this may be true even if the underlying
resource returns false for
HtsQuery.hasIndex()
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hasIndex
public boolean hasIndex()Description copied from interface:HtsQuery
Return true if the underlying resource has an index.- Specified by:
hasIndex
in interfaceHtsQuery<ReferenceSequence>
- Returns:
- true if the underlying resource has an index
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getReferenceSequenceFile
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close
public void close()Description copied from interface:HtsDecoder
Close any resources associated with this decoder.- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceCloseable
- Specified by:
close
in interfaceHtsDecoder<SAMSequenceDictionary,
ReferenceSequence>
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