Changed the way the type of sequence is determined.  Instead of using tokenizers on a string with gaps in them, the sequences of the report is stripped of all gap characters.  Then the string is compared against ATGCU characters in newly written private methods.  The ratio of ATGCU found against the length of the sequence is used. Also, when there are more Us than Cs RNA alphabet is returned.
Changed the way the type of sequence is determined.  Instead of using tokenizers on a string with gaps in them, the sequences of the report is stripped of all gap characters.  Then the string is compared against ATGCU characters in newly written private methods.  The ratio of ATGCU found against the length of the sequence is used.
Also, when there are more Us than Cs RNA alphabet is returned.


git-svn-id: ed25c26de1c5325e8eb0deed0b990ab8af8a4def@1793 7c6358e6-4a41-0410-a743-a5b2a554c398

sbliven/biojava,sbliven/biojava,sbliven/biojava