edu.mssm.crover.webapps.dimlib.util
Class TMValidator

java.lang.Object
  |
  +--edu.mssm.crover.webapps.dimlib.util.TMValidator

public class TMValidator

extends java.lang.Object

Checks if the given TM segment is valid. Returns false if the start or end position is greater than the length of the protein sequence, or if the wildtype residues are not those indicated at the marked position.

Constructor Summary

TMValidator()

Method Summary

static void	main(java.lang.String[] args)
int[]	parseTM(java.lang.String whole_seq, java.lang.String tm, java.lang.String type)
TmDomain_Annotation	parseTMs(java.lang.String whole_seq, java.lang.String tms, java.lang.String type)
java.lang.String	tmToString(java.lang.String seq, int start, int end)
boolean	validateTMDomain(TmDomain_Annotation tm) If segments don't overlap, returns true, else false.

Methods inherited from class java.lang.Object

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

Constructor Detail

TMValidator

public TMValidator()

Method Detail

parseTMs

public TmDomain_Annotation parseTMs(java.lang.String whole_seq,
                                    java.lang.String tms,
                                    java.lang.String type)
                             throws InvalidTMException

InvalidTMException

parseTM

public int[] parseTM(java.lang.String whole_seq,
                     java.lang.String tm,
                     java.lang.String type)
              throws InvalidTMException

InvalidTMException

validateTMDomain

public boolean validateTMDomain(TmDomain_Annotation tm)

If segments don't overlap, returns true, else false.

tmToString

public java.lang.String tmToString(java.lang.String seq,
                                   int start,
                                   int end)

main

public static void main(java.lang.String[] args)