|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biojava3.core.sequence.io.FastaReader<S,C>
public class FastaReader<S extends Sequence<?>,C extends Compound>
Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the primary class used to read Fasta files
Constructor Summary | |
---|---|
FastaReader(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. |
|
FastaReader(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. |
Method Summary | |
---|---|
static void |
main(String[] args)
|
LinkedHashMap<String,S> |
process()
The parsing is done in this method |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public FastaReader(InputStream is, FastaHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator)
br
- headerParser
- sequenceCreator
- public FastaReader(File file, FastaHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator) throws FileNotFoundException
file
- headerParser
- sequenceCreator
-
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.
SecurityException
- if a security manager exists and its checkRead
method denies read access to the file.Method Detail |
---|
public LinkedHashMap<String,S> process() throws IOException
IOException
- if an error occurs reading the input filepublic static void main(String[] args)
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |