[Biojava-l] question regarding MSA

[Mark Chapman]

Hi Bo,

A starting point for formatted output with conservation symbols is already 
implemented for pairwise alignments.  You can try it out by removing one of the 
protein ID's on line 16 of the cookbook code and replacing line 30 with: 
System.out.println(profile.toString(Profile.StringFormat.CLUSTALW));

The code that would need updating for multiple alignments is in 
SimpleProfile.printConservation and around the call to it in the toString helper 
method.

-Mark

On 2/24/2011 2:06 AM, Andreas Prlic wrote:
> Hi Bo Li,
>
> The printing method currently does not add those characters to the
> display of the aligned sequences. If you need it you would have to
> patch the printing method...
>
> Andreas
>
> On Tue, Feb 22, 2011 at 11:16 PM, Bo Li<bli0406 at gmail.com>  wrote:
>> Hi,
>>
>> Sorry for the bothering.  I tried the MSA feature by following the link:
>>
>> http://www.biojava.org/wiki/BioJava:CookBook3:MSA
>>
>> However, I can't see the symbols like ".", ":", and "*" like I can see from
>> the output ClustalW.
>>
>> So is there a way for users to obtain such information in the output from
>> MSA?
>>
>> Thanks,
>> Bo Li
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>
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