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 <[email protected]> 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 <[email protected]> > 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 <[email protected]> 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 <[email protected]> >>> 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 <[email protected]> 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/ > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
