org.biojava.bio.seq.io
Class DefaultDescriptionReader
java.lang.Object
|
+--org.biojava.bio.seq.io.DefaultDescriptionReader
- public class DefaultDescriptionReader
- extends java.lang.Object
- implements FastaDescriptionReader, java.io.Serializable
Assumes that the description is of the form 'id\s*desc'.
- Author:
- Matthew Pocock
- See Also:
- Serialized Form
Method Summary |
void |
parseAnnotation(java.lang.String desc,
Annotation annotation)
Parses annotation out from the description line. |
java.lang.String[] |
parseURNName(java.lang.String desc)
Parses the description line, extracting the names for the URI and name fields. |
java.lang.String |
writeDescription(Sequence seq)
Write the description for a sequence. |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
DefaultDescriptionReader
public DefaultDescriptionReader()
parseURNName
public java.lang.String[] parseURNName(java.lang.String desc)
- Parses the description line, extracting the names for the URI and name fields.
The uri will be of the form urn:sequence/fasta:id
. The name
will be null.
- Specified by:
- parseURNName in interface FastaDescriptionReader
- Tags copied from interface: FastaDescriptionReader
- Parameters:
desc
- the description text from the first non-white space character
after > in the file untill the end of that line- Returns:
- String [] { urn, name }
parseAnnotation
public void parseAnnotation(java.lang.String desc,
Annotation annotation)
- Parses annotation out from the description line.
This will set the id property to the id, and the description property
to everything following the first word.
- Specified by:
- parseAnnotation in interface FastaDescriptionReader
- Tags copied from interface: FastaDescriptionReader
- Parameters:
desc
- the description text from the first non-white space character
after > in the file untill the end of that lineannotation
- the Annotation bundle to modify
writeDescription
public java.lang.String writeDescription(Sequence seq)
- Description copied from interface: FastaDescriptionReader
- Write the description for a sequence.
This should generate a suitable description line, not including the leading
> and spaces, or the trailing newline, and return it as a string.
- Specified by:
- writeDescription in interface FastaDescriptionReader
- Tags copied from interface: FastaDescriptionReader
- Parameters:
seq
- the Sequence to generate a description for- Returns:
- the description text