public abstract class AbstractStringExtractor extends Object implements Enumeration<String>
String
will be treated as in
FastA-format, i.e. lines beginning with ">" will be stripped and
the lines between two ">" (or until the end of the file) will be
appended to form a new String
.Modifier and Type | Field and Description |
---|---|
protected String |
annotation
The annotation of the source.
|
static char |
FASTA
The comment character for FastA-formatted files is ">".
|
protected char |
ignore
The internal comment character.
|
protected Pattern |
ignorePattern
The pattern for ignoring comment lines.
|
static char |
USUALLY
The usual comment character is "#".
|
Modifier | Constructor and Description |
---|---|
protected |
AbstractStringExtractor(char ignore)
Creates a new
AbstractStringExtractor with the specified
character as start of each comment line. |
Modifier and Type | Method and Description |
---|---|
String |
getAnnotation()
Returns the annotation of the source.
|
SequenceAnnotation[] |
getCurrentSequenceAnnotations()
|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
hasMoreElements, nextElement
public static final char USUALLY
public static final char FASTA
String
will be interpreted as in FastA format.protected String annotation
protected Pattern ignorePattern
protected char ignore
protected AbstractStringExtractor(char ignore)
AbstractStringExtractor
with the specified
character as start of each comment line.ignore
- the comment characterPattern
public final String getAnnotation()
public SequenceAnnotation[] getCurrentSequenceAnnotations()
SequenceAnnotation
or null
if no SequenceAnnotation
is available.