Hi Richard,
I have checked out the latest source and tried my code again. It still
didn't work and I received following new errors:
<message>
Exception in thread "main" java.lang.RuntimeException:
java.lang.reflect.InvocationTargetException
at
org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.processFeatureFilter(BioSQLRichSequenceDB.java:143)
at
org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.filter(BioSQLRichSequenceDB.java:151)
at org.sequence_viewer.db.HBioSQLDB.filterFeature(HBioSQLDB.java:612)
at org.sequence_viewer.db.AbfragenTest.main(AbfragenTest.java:56)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at
org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.processFeatureFilter(BioSQLRichSequenceDB.java:138)
... 3 more
Caused by: org.hibernate.PropertyAccessException: Exception occurred
inside setter of org.biojavax.bio.seq.SimpleRichFeature.locationSet
at
org.hibernate.property.BasicPropertyAccessor$BasicSetter.set(BasicPropertyAccessor.java:65)
at
org.hibernate.tuple.entity.AbstractEntityTuplizer.setPropertyValues(AbstractEntityTuplizer.java:337)
at
org.hibernate.tuple.entity.PojoEntityTuplizer.setPropertyValues(PojoEntityTuplizer.java:200)
at
org.hibernate.persister.entity.AbstractEntityPersister.setPropertyValues(AbstractEntityPersister.java:3571)
at
org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:133)
at
org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:854)
at org.hibernate.loader.Loader.doQuery(Loader.java:729)
at
org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236)
at org.hibernate.loader.Loader.doList(Loader.java:2213)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2104)
at org.hibernate.loader.Loader.list(Loader.java:2099)
at
org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:94)
at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1569)
at org.hibernate.impl.CriteriaImpl.list(CriteriaImpl.java:283)
... 8 more
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.GeneratedMethodAccessor18.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at
org.hibernate.property.BasicPropertyAccessor$BasicSetter.set(BasicPropertyAccessor.java:42)
... 21 more
Caused by: java.lang.NullPointerException
at
org.biojavax.bio.seq.PositionResolver$AverageResolver.getMin(PositionResolver.java:103)
at
org.biojavax.bio.seq.SimpleRichLocation.getMin(SimpleRichLocation.java:323)
at
org.biojavax.bio.seq.SimpleRichLocation.overlaps(SimpleRichLocation.java:451)
at
org.biojavax.bio.seq.SimpleRichLocation.union(SimpleRichLocation.java:469)
at org.biojavax.bio.seq.RichLocation$Tools.merge(RichLocation.java:363)
at
org.biojavax.bio.seq.SimpleRichFeature.setLocationSet(SimpleRichFeature.java:181)
... 25 more
<\message>
I think <code> BioSQLFeatureFilter.OverlapsRichLocation(rl) <\code>
causes the problem I have. Can you help me to solve this problem?
I'm grateful for any hints.
cheers,
Gabrielle
Richard Holland schrieb:
This looks like a bug in BJX. I have just committed a fix that I think will
fix it to the head of subversion. Can you check out the latest source,
compile it, and try your program again?
cheers,
Richard
2008/10/9 Gabrielle Doan <[EMAIL PROTECTED]>
Hi Richard,
thanks a lot for your mail. I have successfully retrieved the subsequence
of a sequence as a String. And now I try to get the features for a
particular range with following code:
<code>
public FeatureHolder filterFeature(String name, int startpos, int
endpos) {
RichLocation rl = new SimpleRichLocation(new
SimplePosition(startpos),
new SimplePosition(endpos), 0);
BioSQLFeatureFilter filter = new BioSQLFeatureFilter.And(
new
BioSQLFeatureFilter.BySequenceName(name),
new
BioSQLFeatureFilter.OverlapsRichLocation(rl));
return filter(filter);
}
<\code>
Fortunately I received these errors:
<message>
Exception in thread "main" java.lang.RuntimeException:
java.lang.reflect.InvocationTargetException
at
org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.processFeatureFilter(BioSQLRichSequenceDB.java:143)
at
org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.filter(BioSQLRichSequenceDB.java:151)
at
org.sequence_viewer.db.HBioSQLDB.filterFeature(HBioSQLDB.java:599)
at org.sequence_viewer.db.AbfragenTest.main(AbfragenTest.java:56)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at
org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.processFeatureFilter(BioSQLRichSequenceDB.java:138)
... 3 more
Caused by: org.hibernate.PropertyAccessException: Exception occurred inside
setter of org.biojavax.bio.seq.SimpleRichFeature.locationSet
at
org.hibernate.property.BasicPropertyAccessor$BasicSetter.set(BasicPropertyAccessor.java:65)
at
org.hibernate.tuple.entity.AbstractEntityTuplizer.setPropertyValues(AbstractEntityTuplizer.java:337)
at
org.hibernate.tuple.entity.PojoEntityTuplizer.setPropertyValues(PojoEntityTuplizer.java:200)
at
org.hibernate.persister.entity.AbstractEntityPersister.setPropertyValues(AbstractEntityPersister.java:3571)
at
org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:133)
at
org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:854)
at org.hibernate.loader.Loader.doQuery(Loader.java:729)
at
org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236)
at org.hibernate.loader.Loader.doList(Loader.java:2213)
at
org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2104)
at org.hibernate.loader.Loader.list(Loader.java:2099)
at
org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:94)
at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1569)
at org.hibernate.impl.CriteriaImpl.list(CriteriaImpl.java:283)
... 8 more
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at
org.hibernate.property.BasicPropertyAccessor$BasicSetter.set(BasicPropertyAccessor.java:42)
... 21 more
Caused by: java.lang.NullPointerException
at
org.biojavax.bio.seq.PositionResolver$AverageResolver.getMin(PositionResolver.java:103)
at
org.biojavax.bio.seq.SimpleRichLocation.getMin(SimpleRichLocation.java:323)
at
org.biojavax.bio.seq.SimpleRichLocation.overlaps(SimpleRichLocation.java:451)
at
org.biojavax.bio.seq.SimpleRichLocation.union(SimpleRichLocation.java:469)
at
org.biojavax.bio.seq.RichLocation$Tools.merge(RichLocation.java:363)
at
org.biojavax.bio.seq.SimpleRichFeature.setLocationSet(SimpleRichFeature.java:181)
... 26 more
<\message>
Why do I get these errors?
BioSQLFeatureFilter.BySequenceName(name) needs a seqName as parameter. How
can I find out the sequence name? Is it the value "name" in the table
"Bioentry"? As the build-in subSequence method takes a long time I intend to
get the subsequence as a String by myself and add the features to it. What
do you think about this?
I'm grateful for any hints.
cheers,
Gabrielle
Richard Holland schrieb:
Hello.
Your code is pretty good already - but you're right, it will load the
whole chromosome into memory before you can chop out the interesting
bit you actually need.
As you observed, by using ThinRichSequence in your query it will load
only the initial shell of a sequence object to start with, but the
moment you try and sub-sequence it, it will immediately load the whole
sequence data into memory in order to perform the operation.
If you only want the sequence data, as a string, you can do this by
specifying the sequence attribute in the query and bypassing the
sequence object entirely:
select rs.stringSequence from Sequence as rs where rs.description
like '%hromosome :num%
This will return a String instead of a RichSequence object. You can
use HQL operators to perform substrings etc. on the string inside the
query itself - see
http://docs.huihoo.com/hibernate/hibernate-reference-3.2.1/queryhql.html
, particularly section 14.9.
If you only want the features, you can do this by using the
BioSQLFeatureFilter technique. In particular you will want the
BySequenceName filter, the And filter, and the OverlapsRichLocation
filter. You construct a filter then pass it to the filter() method in
BioSQLRichSequenceDB. The database will return to you all the
RichFeature objects that match your criteria. Note that it searches
the whole database so you really must use a BySequenceName filter at
the very least in order to make the results useful!
However, you can't use HQL to construct a complete slice of a sequence
directly in the database before returning it to the program for use as
a ready-made RichSequence object. This would require Hibernate to know
what a BioJava sub-sequence object is and how it behaves in relation
to an 'unsliced' one, which is beyond the scope of it's job as a
persistence framework.
cheers,
Richard
2008/10/7 Gabrielle Doan <[EMAIL PROTECTED]>:
Hi all,
I have a BioSQL database which contains all human chromosomes. My
intention
is to get the information about a particular gene. How can I get a part
of a
particular chromosome with all associated features? At the moment I use
following code to create my new sequence:
<code>
RichSequence subSeq = RichSequence.Tools.subSequence(parent,
position[0], position[1], ns, geneName, parent.getAccession(),
parent.getIdentifier(), parent.getVersion() + 1,
(Double) (parent.getVersion() + 1.0));
<\code>
Here is the part how I get the parent sequence:
<code>
public static RichSequence getChromosome(String chrNo) {
Transaction tx = session.beginTransaction();
RichSequence ret = null;
String query;
try {
if (chrNo.equals("MT")) {
query = "from BioEntry as be where
be.description like '%:num%'";
query = query.replaceAll(":num",
"mitochondrion");
} else {
query = "from BioEntry as be where
be.description like '%hromosome :num%'";
query = query.replaceAll(":num", chrNo);
}
Query q = session.createQuery(query);
ret = (RichSequence) q.list().get(0);
tx.commit();
} catch (Exception e) {
tx.rollback();
e.printStackTrace();
}
return ret;
}
<\code>
I always have to load the whole chromsome to get a part of it, so it
takes
very long time and I get a lot of unused information (waste of memory). I
also tried to use <code>ThinRichSequence<\code> instead of
<code>RichSequence<\code>, but thereby I didn't notice any difference.
Can you give me a hint how to accelerate the code?
I am grateful for any hits.
cheers,
Gabrielle
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