[Biojava-dev] (no subject)

[Singh, Nimesh]

Hi,
 
The MSFAlignmentFormat and FastaAlignmentFormat classes put the sequences into a HashMap to create the Alignment.  Could we instead use a LinkedHashMap, to maintain insertion order of sequences in the alignment.  This would allow an iterator over the sequences in the alignment to go in the same order as in the original file.
 
The lines that would need to change are line 173 in the MSFAlignmentFormat class, and line 70 in the FastaAlignmentFormat class, changing the word HashMap to LinkedHashMap.
 
Also, last summer I worked with biojava a bit and had a read/write account, but that has either been deactivated or I forgot my password, so can I have one again?  My username was nks31, I believe.
 
Thanks,
Nimesh Singh