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java.lang.Objectdata.FASTAParser
public class FASTAParser
Reads sequences in (multi-)FASTA format. Deletes translation stop character (*) at the end of a sequence.
This class provides static methods only and cannot be instantiated.
Sequences
Method Summary | |
---|---|
static Sequences |
loadSequences(InputStream input)
Loads sequences from a given InputStream, requires multi-FASTA format data |
static Sequences |
loadSequences(InputStream input,
String organism)
Loads sequences from a given InputStream, requires multi-FASTA format data |
static Sequences |
loadSequences(String file)
Loads sequences from a given multi-FASTA file |
static Sequences |
loadSequences(String file,
String organism)
Loads sequences from a given multi-FASTA file |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static Sequences loadSequences(String file) throws IOException
file
- path to the FASTA file
Sequences
object containing the read sequences
IOException
- if the file could not be readpublic static Sequences loadSequences(String file, String organism) throws IOException
file
- path to the FASTA fileorganism
- optional organism identifier, null is treated as no organism (see also: ProteinManager
)
Sequences
object containing the read sequences
IOException
- if the file could not be readpublic static Sequences loadSequences(InputStream input) throws IOException
input
- input stream from which the sequence data will be read
Sequences
object containing the read sequences
IOException
public static Sequences loadSequences(InputStream input, String organism) throws IOException
input
- input stream from which the sequence data will be readorganism
- specify an organism identifier for the new proteins or null for no organism (see also: ProteinManager
)
Sequences
object containing the read sequences
IOException
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