Constructor and Description |
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FastaReader(java.io.File file,
FastaHeaderParserInterface<S,C> headerParser,
SequenceCreatorInterface<C> sequenceCreator)
If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about
the location of the file.
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FastaReader(java.io.InputStream is,
FastaHeaderParserInterface<S,C> headerParser,
SequenceCreatorInterface<C> sequenceCreator)
If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about
local file offsets for quick reads.
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public FastaReader(java.io.InputStream is, FastaHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator)
br
- headerParser
- sequenceCreator
- public FastaReader(java.io.File file, FastaHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator) throws java.io.FileNotFoundException
file
- headerParser
- sequenceCreator
- java.io.FileNotFoundException
- if the file does not exist, is a directory
rather than a regular file, or for some other reason cannot be opened
for reading.java.lang.SecurityException
- if a security manager exists and its checkRead
method denies read access to the file.public java.util.LinkedHashMap<java.lang.String,S> process() throws java.io.IOException
java.io.IOException
- if an error occurs reading the input filepublic static void main(java.lang.String[] args)