de.zimek.proteinfeatures.parser
Class DSSPInterpreter

java.lang.Object
  de.zimek.proteinfeatures.parser.DSSPInterpreter

public class DSSPInterpreter

extends java.lang.Object

Author:

Arthur Zimek

Field Summary

private char[]

ss

Constructor Summary

DSSPInterpreter(java.lang.String dssp)

DSSPInterpreter(java.lang.String dssp, boolean interpret)

Method Summary

protected int	checkFor(char symbol, int index) Returns length of sequence of given symbol starting with index in ss.
java.lang.String	getSS()
protected void	interpretSS() Interprets ss according to following rules: 'H' is accepted if the sequence of 'H's is at least of length 5.
protected void	setCoil(int index, int length)
protected void	translateSS()

Methods inherited from class java.lang.Object

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

Field Detail

ss

private char[] ss

Constructor Detail

DSSPInterpreter

public DSSPInterpreter(java.lang.String dssp)
                throws java.lang.IllegalArgumentException

DSSPInterpreter

public DSSPInterpreter(java.lang.String dssp,
                       boolean interpret)

Method Detail

translateSS

protected void translateSS()
                    throws java.lang.IllegalArgumentException

Throws:

java.lang.IllegalArgumentException

interpretSS

protected void interpretSS()

Interprets ss according to following rules: 'H' is accepted if the sequence of 'H's is at least of length 5. 'E' is accepted if the sequence of 'E's is at least of length 3.

setCoil

protected void setCoil(int index,
                       int length)

checkFor

protected int checkFor(char symbol,
                       int index)

Returns length of sequence of given symbol starting with index in ss.

Parameters:

symbol -

index -

Returns:

int

getSS

public java.lang.String getSS()