[Biojava-l] Chromatagraph reading in BioJava3?

[Nick England]

If I try to run maven I got the following:

[INFO] Building sequence analysis 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: http://www.biojava.org/download/maven/org/biojava/biojava-legacy/1.8.2/biojava-legacy-1.8.2.pom
Downloading: http://repo.maven.apache.org/maven2/org/biojava/biojava-legacy/1.8.2/biojava-legacy-1.8.2.pom
[WARNING] The POM for org.biojava:biojava-legacy:jar:1.8.2 is missing,
no dependency information available
Downloading: http://www.biojava.org/download/maven/org/biojava/biojava-legacy/1.8.2/biojava-legacy-1.8.2.jar
Downloading: http://repo.maven.apache.org/maven2/org/biojava/biojava-legacy/1.8.2/biojava-legacy-1.8.2.jar
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE

I get this for 1.8 and 1.8.1 as well:

Could not find artifact org.biojava:biojava-legacy:jar:1.8 in
biojava-maven-repo (http://www.biojava.org/download/maven/) -> [Help
1]
Could not find artifact org.biojava:biojava-legacy:jar:1.8.1 in
biojava-maven-repo (http://www.biojava.org/download/maven/) -> [Help
1]

If I try to install it from source, I'm getting some class cast
exceptions during the unit tests for some tests in core:

Failed tests:
  testGetNoteSet(org.biojavax.bio.SimpleBioEntryTest)
  testGetRankedCrossRefs(org.biojavax.bio.SimpleBioEntryTest)


3.0 works fine, but lacks the class I want!.
Presumably BioJava 1.8 hasn't always been called biojava-legacy? Since
maven releases should be immutable, it should still be available from
the original release maven repo?

Thanks for the help,

Nick


On 12 March 2012 20:38, Andreas Prlic <andreas at sdsc.edu> wrote:
>> 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
>>>
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