public interface FASTAFile extends Serializable, Cloneable, Set<FASTAElement>
FASTAFile
is a collection of FASTAElement
s, that includes some information for serialization and string
representation.
last reviewed: 2013-04-29
FASTAElement
Modifier and Type | Field and Description |
---|---|
static int |
DEFAULT_LINE_LENGTH
Default number of characters to write to one line.
|
static char |
HEADER_IDENT
First character of header line that will identify
FASTAElement 's
header line. |
Modifier and Type | Method and Description |
---|---|
FASTAElement |
getElementByHeader(String header)
Retrieves
FASTAElement with given header string, if
there is such an element. |
FASTAElement |
getLargestElement()
Retrieves Element with the longest sequence.
|
int |
getLineLength()
Retrieves this
FASTAFile 's line length. |
boolean |
hasElementByHeader(String header)
Checks whether this
FASTAFile contains a FASTAElement
with given header string. |
void |
setLineLength(int len)
Sets this
FASTAFile 's line length. |
static final char HEADER_IDENT
FASTAElement
's
header line.static final int DEFAULT_LINE_LENGTH
DEFAULT_LINE_LENGTH
characters, a
NEW_LINE_STRING
will be appended.FASTAElement getElementByHeader(String header)
FASTAElement
with given header string, if
there is such an element.header
- header string that matches returned FASTAElement
's header stringFASTAElement
which header matches given oneNoSuchElementException
- if there is no such elementFASTAElement getLargestElement()
FASTAElement
with the longest sequenceint getLineLength()
FASTAFile
's line length.FASTAFile
's line lengthboolean hasElementByHeader(String header)
FASTAFile
contains a FASTAElement
with given header string.header
- header stringFASTAElement
in this
FASTAFile
, false otherwisevoid setLineLength(int len)
FASTAFile
's line length.len
- line length to useCopyright © 2013. All Rights Reserved.