two sequences of same name in one file

[GoogleCodeExporter]

What steps will reproduce the problem?
1. add two sequences of same name in  a file, and concat it with another file.
2.
3.

What is the expected output? What do you see instead?
all sequences are expected to be the same length. the sequence with two
copies in one file is longer, and aligning weird.

What version of the product are you using? On what operating system?
v2.2 on Ubuntu 7.10

Please provide any additional information below.
This is not a problem with the code. An error message stating that there
are two sequences of same name in one file would be nice.

Original issue reported on code.google.com by erem.kaz...@gmail.com on 4 Apr 2008 at 9:21

[GoogleCodeExporter]

this is being worked on, though a general solution is hard, so instead there 
will be
a notification of the issue to the user

Original comment by blackrim on 8 Apr 2010 at 2:45

[GoogleCodeExporter]

Original comment by blackrim on 8 Apr 2010 at 2:46

• Changed state: Started

[GoogleCodeExporter]

Original comment by blackrim on 29 Jan 2012 at 11:29

• Changed state: Done