[Biojava-l] Writing EMBL files

Hello, We are loading an EMBL file into a SequenceDB and then writing it out again and getting the following error: 16:42:19,032 INFO [STDOUT] at org.biojava.bio.seq.io.EmblFileFormer.addSequ enceProperty(EmblFileFormer.java:246) 16:42:19,032 INFO [STDOUT] at org.biojava.bio.seq.io.Se

[Biojava-l] Serialization of RemoteFeature.Region

Hello, Serialization buff that I am, it's a wonder this one slipped past me earlier. RemoteFeature.Region won't serialize. Could this inner class be made serializable - some sequences obtained from Genbank won't serialize because of this. Cheers, Vasa

Re: [Biojava-l] Serialization of SequenceDB obtained from Swiss-Prot

ature. Regards, Vasa Schreiber, Mark wrote: Hi - I'm not sure serializing an entire SequenceDB is a good idea, however, can you tell me if the serialization is failing on the DB or one of the sequences in it? - Mark -Original Message----- From: Vasa Curcin [mailto:[EMAIL PROTECTED] Sen

[Biojava-l] Serialization of SequenceDB obtained from Swiss-Prot

Hello, There seems to be some problem with serializing SequenceDB objects obtained from SwissProtDatabase. The error is: java.io.WriteAbortedException: writing aborted; java.io.NotSeria lizableException: org.biojava.bio.seq.io.SequenceBuilderBase$TemplateWithChildre n at java.io.ObjectI

[Biojava-l] NCBI database

Hello, It seems that the NCBI class is not working anymore. I am using it to retrieve some annotated sequences, and since this morning it is returning a MalformedURLException. It seems like the web interface to NCBI changed. Anyone knows something about this? Regards, Vasa

[Biojava-l] Serialization of SimpleSequences

Hello, While transferring some sequences via serialization, I noticed that all my Features are getting lost. After some digging around, it seems as if Java doesn't serialize the FeatureHolder inside the sequence (I was working with SimpleSequence objects). Even though a NotSerializableExceptio

Re: [Biojava-l] RE: Sequence serialization exception - AlphabetManagerproblem?

Having exactly the same problem here with serializing SimpleSequence objects containing proteins. It doesn't like MET... Was there a solution found? Vasa Schreiber, Mark wrote: Hi - I am not getting the exception you have below (which looks like one from before we fixed the EmblFileFormer). I

[Biojava-l] Connection to DAS servers

Hi, Trying to connect to this DAS server running dazzle, and it retrieves the sequences, but they seem to be malformed - there is some error regarding the 'stretch'. Has anyone experienced something similar with regards to DAS? Cheers, Vasa ___ Bioja

[Biojava-l] Question about Swiss-Prot parsing

Hello, I am parsing some Swiss-Prot files with Biojava 1.3 and need to put the contents into Sequence Collections. It does not crash but there are two problems: 1. Each annotation is shown as the tag, followed by a colon and then the content, so for example AC :Q9L867. Other parsers seem to be

[Biojava-l] Serialisation of Sequences

Is there any issue that would cause Features not be written to file with standard Java serialisation? I am writing SequenceDB objects, and everything seems fine upon loading, except that the sequences have lost all the Features placed on them. Any ideas? Cheers, Vasa ___

[Biojava-l] PDB file import

Is PDB file import working? Invoking: SequenceFormat sf = SeqIOTools.getSequenceFormat(SeqIOConstants.PDB); Returns: org.biojava.bio.BioException: No SequenceFormat available for format/alphabet identifier '524309' Anyone else has this problem? Vasa _

[Biojava-l] Dox on biojava.org

Is it just me or are the .html files for the stable 1.30 version in docs section all 0KB in length? Vasa ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l