[Biojava-l] Simple alignment

[Michael Heuer]

I think it might make more sense to create an interface OrderedAlignment
as you suggest than to change an implementation detail in the existing
code.

   michael


On Mon, 15 Sep 2003, Emig, Robin wrote:

> 	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.
> -Robin
>
> -----Original Message-----
> 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?
>
> Matthew
>
> Schreiber, Mark wrote:
>
> >Robin -
> >
> >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.
> >
> >- Mark
> >
> >
> >
> >-----Original Message-----
> >From: Emig, Robin [mailto:Robin.Emig at maxygen.com]
> >Sent: Mon 15/09/2003 3:04 p.m.
> >To: bio java
> >Cc:
> >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.
> >	-Robin
> >
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