|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectde.jstacs.io.StringExtractor
public class StringExtractor
This class implements the reader that extracts strings from either a file or a string. 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 | |
---|---|
static char |
FASTA
The comment-character for FastA-formatted files is '>'. |
static char |
USUALLY
The usual comment-character is #. |
Constructor Summary | |
---|---|
StringExtractor(File file,
int initSize)
A constructor that reads the lines from file . |
|
StringExtractor(File file,
int initSize,
char ignore)
A constructor that reads the lines from file and ignores those starting with ignore . |
|
StringExtractor(File file,
int initSize,
char ignore,
String annotation)
A constructor that reads the lines from file and ignores those starting with ignore . |
|
StringExtractor(File file,
int initSize,
String annotation)
A constructor that reads the lines from file . |
|
StringExtractor(String content,
int initSize,
char ignore,
String annotation)
A constructor that reads the lines from a String content and ignores those starting with ignore |
|
StringExtractor(String content,
int initSize,
String annotation)
A constructor that reads the lines from a String content . |
Method Summary | |
---|---|
String |
getAnnotation()
Returns the annotation of the source. |
int |
getNumberOfStrings()
Returns the number of strings |
String |
getString(int i)
Returns the string with index i . |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
public static char USUALLY
public static char FASTA
Constructor Detail |
---|
public StringExtractor(File file, int initSize) throws IOException, FileNotFoundException
file
.
file
- the file to be read frominitSize
- the inital number of lines the can be handled
IOException
- is thrown if the file could not be read
FileNotFoundException
- is thrown if the file could not be foundpublic StringExtractor(File file, int initSize, char ignore) throws IOException, FileNotFoundException
file
and ignores those starting with ignore
.
file
- the file to be read frominitSize
- the inital number of lines the can be handledignore
- the first character of lines that should be treated as comments
IOException
- is thrown if the file could not be read
FileNotFoundException
- is thrown if the file could not be foundpublic StringExtractor(File file, int initSize, String annotation) throws IOException, FileNotFoundException
file
.
file
- the file to be read frominitSize
- the inital number of lines the can be handledannotation
- the annotation for the source
IOException
- is thrown if the file could not be read
FileNotFoundException
- is thrown if the file could not be foundpublic StringExtractor(File file, int initSize, char ignore, String annotation) throws IOException, FileNotFoundException
file
and ignores those starting with ignore
.
file
- the file to be read frominitSize
- the inital number of lines the can be handledignore
- the first character of lines that should be treated as commentsannotation
- the annotation for the source
IOException
- is thrown if the file could not be read
FileNotFoundException
- is thrown if the file could not be foundpublic StringExtractor(String content, int initSize, String annotation)
content
.
content
- the complete String with all linesinitSize
- the inital number of lines the can be handledannotation
- some annotation for the contentpublic StringExtractor(String content, int initSize, char ignore, String annotation)
content
and ignores those starting with ignore
content
- the complete String with all linesinitSize
- the inital number of lines the can be handledignore
- the first character of lines that should be treated as commentsannotation
- some annotation for the contentMethod Detail |
---|
public String getString(int i)
i
.
i
- the index
i
public int getNumberOfStrings()
public String getAnnotation()
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |