[Biojava-l] Simple alignment
Robin.Emig at maxygen.com
Mon Sep 15 11:18:34 EDT 2003
Well, The problem is that the code in biojava is "safe", so it copies the Map first thing, but it copies it into a HashMap. So, since what I really need is the have the same order from an iterator that the file was read, all that needs to be done is to have all instances of HashMap in MSFAlignmentFormat, FastaAlignmentFormat and SimpleAlignment to be changed to LinkedHashMap. Then there should be no changes needed to any "interfaces". I think we should also have a unit test built to verify this as well.
From: Matthew Pocock [mailto:matthew_pocock at yahoo.co.uk]
Sent: Monday, September 15, 2003 2:13 AM
To: Schreiber, Mark
Cc: Emig, Robin; bio java
Subject: Re: [Biojava-l] Simple alignment
Doesn't TreeMap extend/implement Map? Is there a reason you can't just
pass a TreeMap into the constructor?
Schreiber, Mark wrote:
>How about overloading the constructor? That way if you provide a TreeMap the result is ordered. If not you get what you get. Many classes are dependent on SimpleAlignment so it may not pay to change it too much.
>From: Emig, Robin [mailto:Robin.Emig at maxygen.com]
>Sent: Mon 15/09/2003 3:04 p.m.
>To: bio java
>Subject: [Biojava-l] Simple alignment
> Is there any objection to making SimpleAlignment take a TreeMap instead of a simple Map? The reason is that order of the sequences in the alignment is often of importance. I suppose the alternative is to create a new alignment called OrderedAlignment.
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