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java.lang.Objectde.jstacs.io.AbstractStringExtractor
public abstract class AbstractStringExtractor
This class implements the reader that extracts strings. The class ignores
lines starting with a given character, since those lines are treated as
comments. If the user does not specify this character, it is set to
"#" internally. If the user specifies this character as
">", the file or 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
.
Field Summary | |
---|---|
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 "#". |
Constructor Summary | |
---|---|
protected |
AbstractStringExtractor(char ignore)
Creates a new AbstractStringExtractor with the specified
character as start of each comment line. |
Method Summary | |
---|---|
String |
getAnnotation()
Returns the annotation of the source. |
SequenceAnnotation[] |
getCurrentSequenceAnnotations()
Returns the SequenceAnnotation or null if no SequenceAnnotation is available. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface java.util.Enumeration |
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hasMoreElements, nextElement |
Field Detail |
---|
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
Constructor Detail |
---|
protected AbstractStringExtractor(char ignore)
AbstractStringExtractor
with the specified
character as start of each comment line.
ignore
- the comment characterPattern
Method Detail |
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public final String getAnnotation()
public SequenceAnnotation[] getCurrentSequenceAnnotations()
SequenceAnnotation
or null
if no SequenceAnnotation
is available.
SequenceAnnotation
or null
if no SequenceAnnotation
is available.
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