That is a limitation for string literals, not any string. Correct?
On Fri, Jul 18, 2008 at 4:47 AM, Richard Holland <[EMAIL PROTECTED]> wrote: > In order to persist to BioSQL, BioJava has to convert the symbol list > into a string so that it can pass it to JDBC via Hibernate. Therefore > the maximum length of a sequence you wish to persist to BioSQL is the > maximum length of a string in Java, which is 65536 (2^16) if you are > working in a UTF-8 environment. > > 2008/7/18 Rey Vincent Babilonia <[EMAIL PROTECTED]>: >> Hi Mark, >> >> What is the maximum sequence length that a RichSequence can handle? >> >> java -Xms1024m -Xmx1256m -jar loader.jar >> . >> 16:09:00,173 INFO Loader:296 - D:\AE005174.gbk is readable. >> 16:09:06,704 INFO Loader:326 - Loading sequence AE005174 with identifier >> 56384585, length 5528445 and alphabet DNA... >> org.hibernate.PropertyAccessException: Exception occurred inside getter of >> org.biojavax.bio.seq.SimpleRichSequence.sequenceLength >> >> Rey Vincent Babilonia wrote: >>> >>> Hi Mark, >>> >>> At first it throws an out of memory exception. My workaround is to >>> subdivide the sequence file into individual GenBank files. >>> >>> The error now is that if a GenBank sequence has an 'empty alphabet', it >>> does not get loaded to BioSQL. My workaround is to check if >>> sequence.getAlphabet().getName() is DNA. >>> >>> Thanks. >>> >>> Mark Schreiber wrote: >>>> >>>> Hi - >>>> >>>> Is the code throwing an exception or running out of memory?? >>>> >>>> Can you send an example program and the problem you encounter to the >>>> list. >>>> - Mark >>>> >>>> On Thu, May 29, 2008 at 9:53 AM, Rey Vincent Babilonia >>>> <[EMAIL PROTECTED]> wrote: >>>>> >>>>> -------- Original Message -------- >>>>> Subject: large genbank data >>>>> Date: Wed, 28 May 2008 18:02:48 +0800 >>>>> From: Rey Vincent Babilonia <[EMAIL PROTECTED]> >>>>> To: [EMAIL PROTECTED] >>>>> >>>>> hi, >>>>> >>>>> anybody tried uploading a large genbank data (e.g. >>>>> ftp://bio-mirror.net/biomirror/genbank/gbbct1.seq.gz) to biosql? >>>>> load_seqdatabase.pl of bioperl can do this. i'm switching to biojava and >>>>> it can't read the sequence (maybe because it has 30000+ sequences). >>>>> >>>>> thanks. >>>>> >>>>> -- >>>>> /** >>>>> * @author Rey Vincent P. Babilonia >>>>> * @number +63 2 426 9760 local 1302 >>>>> * @pgp 0x383454CF <at> pgp.mit.edu >>>>> * @project Philippine Bioinformatics Solutions >>>>> * @program Philippine e-Science Grid >>>>> * @division Research and Development Division >>>>> * @agency Advanced Science and Technology Institute >>>>> * @url http://www.psigrid.gov.ph >>>>> */ >>>>> >>>>> >>>>> -- >>>>> /** >>>>> * @author Rey Vincent P. Babilonia >>>>> * @number +63 2 426 9760 local 1302 >>>>> * @pgp 0x383454CF <at> pgp.mit.edu >>>>> * @project Philippine Bioinformatics Solutions >>>>> * @program Philippine e-Science Grid >>>>> * @division Research and Development Division >>>>> * @agency Advanced Science and Technology Institute >>>>> * @url http://www.psigrid.gov.ph >>>>> */ >>>>> >>>>> No virus found in this outgoing message. >>>>> Checked by AVG. >>>>> Version: 8.0.100 / Virus Database: 269.24.2/1471 - Release Date: >>>>> 5/28/2008 5:33 PM >>>>> >>>>> _______________________________________________ >>>>> biojava-dev mailing list >>>>> [EMAIL PROTECTED] >>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>>>> >>>> >>> >> >> -- >> /** >> * @author Rey Vincent P. Babilonia >> * @number +63 2 426 9760 local 1302 >> * @pgp 0x383454CF <at> pgp.mit.edu >> * @project Philippine Bioinformatics Solutions >> * @program Philippine e-Science Grid >> * @division Research and Development Division >> * @agency Advanced Science and Technology Institute >> * @url http://www.psigrid.gov.ph >> */ >> >> _______________________________________________ >> biojava-dev mailing list >> [EMAIL PROTECTED] >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
