de.jstacs.io
Class SymbolExtractor

java.lang.Object
  de.jstacs.io.SymbolExtractor

All Implemented Interfaces:

Enumeration<String>

public class SymbolExtractor
extends Object
implements Enumeration<String>

This class enables you to extract elements form a given string similar to an StringTokenizer.

The class has some special functionalities that are not given be a StringTokenizer:

1. It enables you to recycle use objects.
2. It handles the delimiter "", null. (In this case the characters of the string are returned.)

   Author:

   Jens Keilwagen

   Constructor Summary

   SymbolExtractor(String delim)
   Creates a new instance using delim as delimiter.

   SymbolExtractor(String string, String delim)
   Creates a new instance using delim as delimiter and string as string to be parsed.

   Method Summary

   int	countElements() Counts the number of elements that can initially be received.
   static int	filter(String inFile, char ignore, AlphabetContainer con, int minLength, String outFile) This method allows the user to filter a file using a given alphabet container and a minimal sequence length.
   boolean	hasMoreElements()
   String	nextElement()
   void	setStringToBeParsed(String string) Sets a new string to be parsed.

   Methods inherited from class java.lang.Object

   clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

   Constructor Detail

   SymbolExtractor

   public SymbolExtractor(String delim)

   Creates a new instance using delim as delimiter. Before invoking other methods one has to use setStringToBeParsed(String)

   Parameters:

   delim - the delimiter

   See Also:

   setStringToBeParsed(String)

   SymbolExtractor

   public SymbolExtractor(String string,
                          String delim)

   Creates a new instance using delim as delimiter and string as string to be parsed.

   Parameters:

   string - the string to be parsed

   delim - delimiter

   Method Detail

   setStringToBeParsed

   public void setStringToBeParsed(String string)

   Sets a new string to be parsed.

   Parameters:

   string - the string to be parsed

   countElements

   public int countElements()

   Counts the number of elements that can initially be received.

   Returns:

   the number of elements that can initially be received

   hasMoreElements

   public boolean hasMoreElements()

   Specified by:

   hasMoreElements in interface Enumeration<String>

   nextElement

   public String nextElement()

   Specified by:

   nextElement in interface Enumeration<String>

   filter

   public static int filter(String inFile,
                            char ignore,
                            AlphabetContainer con,
                            int minLength,
                            String outFile)
                     throws IOException

   This method allows the user to filter a file using a given alphabet container and a minimal sequence length. This method is useful to filter for instance data sets with ambiguous nucleotides and/or short sequences. Lines that can not be parsed with respect to the alphabet container will be masked by the ignore char.

   Parameters:

   inFile - the input file

   ignore - the char for comment lines

   con - the alpgabet container

   minLength - the minimal length of a sequence in the output file

   outFile - the output file

   Returns:

   the number of discarded lines

   Throws:

   IOException - if something with the file handling went wrong