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)


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.