[Biojava-l] Chromatagraph reading in BioJava3?

[Michael Heuer]

Hello Andreas,

I noticed this in the pom for das 1.8.2-SNAPSHOT

<dependency>
  <groupId>org.biojava</groupId>
  <artifactId>biojava3-structure</artifactId>
  <version>3.0-alpha1</version>
  <scope>compile</scope>
</dependency>

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.

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
>
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