[Biojava-l] BioJava Help

[Andreas Prlic]

Hi Omer,

please keep such questions on the public list. Chances are high that
if you are struggling with something, somebody else is having the same
problem as well.

I wasactually talking about BioJava 1.8, the previous version of
BioJava. It is still available and the cookbook page that I meant is
here:
http://biojava.org/wiki/BioJava:CookBook:Blast:Parser

About Maven: It is probably best to start with a new project in your
favorite IDE and set it up as a Maven project that depends on BioJava.
(i.e. add the BioJava repository to the pom configuraiton). If you
think this is difficult, we can/should set up a documentation page
that explains those first steps.

Andreas



On Tue, Oct 11, 2011 at 6:34 AM, Omer Eilam <omereila at post.tau.ac.il> wrote:
> Are you referring to the BlastXMLQuery class? because I see in the API
> that it contains only one method.
> Also, I am not familiar with using Maven, I see the various biojava
> packages in the eclipse project explorer, but I don't know how to
> create a new class (i.e. do I need imports and stuff?)
>
> Thanks again!
> omer
>
> On Mon, Oct 10, 2011 at 3:58 AM, Andreas Prlic <andreas.prlic at gmail.com> wrote:
>> Hi Omer,
>>
>> Our recommendation nowadays for working with Blast is to get XML
>> output and simply parse that. Depending on what you need that will
>> give you more details than the parser that is in the BioJava 1.8
>> (legacy) project. (if you still want to give that one a try, there is
>> a cookbook page for it)
>>
>> Andreas
>>
>>
>> On Sun, Oct 9, 2011 at 2:26 AM, Omer Eilam <omereila at post.tau.ac.il> wrote:
>>> I eventually succeeded in importing Biojava.
>>> I read in the paper that there is a parser for BLAST - where can I get
>>> more information/API on this?
>>>
>>> Thanks!
>>> omer
>>>
>>> On Thu, Oct 6, 2011 at 5:35 PM, Andreas Prlic <andreas.prlic at gmail.com> wrote:
>>>> Hi Omer,
>>>>
>>>> We are having problems with the anonymous SVN server quite often. I
>>>> recommend trying the git copy at github, or their SVN interface, or
>>>> using Maven to install it.
>>>>
>>>> http://www.biojava.org/wiki/CVS_to_SVN_Migration
>>>>
>>>> Andreas
>>>>
>>>> On Thu, Oct 6, 2011 at 1:56 AM, Omer Eilam <omereila at post.tau.ac.il> wrote:
>>>>> Dear Andreas,
>>>>>
>>>>> I wish to install BioJava for my eclipse IDE.
>>>>> I followed all the instructions in the website
>>>>> http://www.biojava.org/wiki/BioJava3_eclipse.
>>>>> I currently have problems with the last step. I create a new Maven
>>>>> project, but when I try to type /biojava/biojava-live/trunk in the SCM
>>>>> URL, I get an "invalid URL" error.
>>>>> Please let me know what seems to be the problem and how can I fix it.
>>>>>
>>>>> Thanks much!
>>>>> omer
>>>>>
>>>>> --
>>>>> Omer Eilam
>>>>> Complex Network Systems
>>>>> Prof. Eytan Ruppin
>>>>> Tel-Aviv University
>>>>> http://cns.cs.tau.ac.il/
>>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> Omer Eilam
>>> Complex Network Systems
>>> Prof. Eytan Ruppin
>>> Tel-Aviv University
>>> http://cns.cs.tau.ac.il/
>>>
>>
>
>
>
> --
> Omer Eilam
> Complex Network Systems
> Prof. Eytan Ruppin
> Tel-Aviv University
> http://cns.cs.tau.ac.il/
>