[Biojava-l] Chromatagraph reading in BioJava3?

[Andreas Prlic]

> I don't think that would cause trouble as reported below, but it is
> odd in any case.  1.8.x shouldn't have a dependency on 3.x.

In principle I agree, however there are historic reasons for this.  If
this config causes a problem then I would vote for removing it. The
biojava-legacy project contains no structure sources any more since it
was completely upgraded into the 3.X series. The API is compatible to
a large extent.  There is no reason for anybody to still be using a
1.X version of structure.

Andreas



> Hello Nick,
>
> What kind of maven failure are you seeing?
>
>   michael
>
>
> On Mon, Mar 12, 2012 at 12:54 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> I am not aware of any issues with that. Does either 1.8 or
>> 1.8.2-SNAPSHOT work? Depending on your IDE, you just might have to
>> refresh your Maven dependencies?
>>
>> Andreas
>>
>>
>>
>> On Mon, Mar 12, 2012 at 10:39 AM, Nick England <nickengland at gmail.com> wrote:
>>> Thanks for the help, 1.8.1 seems to have the classes I need. But I
>>> haven't been able to get maven to work with biojava 1.8. It works fine
>>> with 3.X, but when I try to use the dependency:
>>>                <dependency>
>>>                        <groupId>org.biojava</groupId>
>>>                        <artifactId>biojava-legacy</artifactId>
>>>                        <version>1.8.1</version>
>>>                </dependency>
>>> it fails, even though there appears to be the corresponding pom on the
>>> repository at http://www.biojava.org/download/maven/org/biojava/biojava-legacy/1.8.1/
>>>
>>> I have the repo at :
>>>                 <repository>
>>>                        <id>biojava-maven-repo</id>
>>>                        <name>BioJava repository</name>
>>>                        <url>http://www.biojava.org/download/maven/</url>
>>>                </repository>
>>>
>>> Am I doing something wrong, or has the release version 1.8.1 somehow
>>> broken on the repository?
>>>
>>> Thanks,
>>>
>>> Nick
>>>
>>> On 12 March 2012 16:43, Andreas Prlic <andreas at sdsc.edu> wrote:
>>>> Hi Nick,
>>>>
>>>> this feature has not been ported to biojava3 so far and you can get it
>>>> via biojava 1.8.1
>>>>
>>>> Andreas
>>>>
>>>> On Mon, Mar 12, 2012 at 8:04 AM, Nick England <nickengland at gmail.com> wrote:
>>>>> Hello all,
>>>>>
>>>>> I am trying to read some .scf files into BioJava3. I have found the
>>>>> example code for 1.3
>>>>> (http://biojava.org/wiki/BioJava:Cookbook:SeqIO:ABItoSequence) but I
>>>>> can't find any classes in the 3.0 API which look at all related to
>>>>> those ones. Is it possible, or should I downgrade to 1.3 if I want to
>>>>> be able to read .scf files?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Nick
>>>>> _______________________________________________
>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l