[Biojava-l] problem with AnnotationBuilder?

[Matthew Pocock]

Hi francois,

The documentation here is not good. The default behavior of the 
annotation builder is to simply replace the properties as it goes. If 
you want list-building behavior, then you can configure this. For 
example, create a new AnnotationType where you explicitly set the type 
of NAME to being an un-bounded list of strings.

AnnotationType annT = new AnnotationType.Impl();
PropertyConstraint c_string = new PropertyConstraint.ByClass(String.class);
annT.setConstraints("NAME", c_string, CardinalityConstraint.ONE_OR_MORE);

Now, when top.type.setProperty() is invoked, it will end up routing each 
value to an object that knows that the values in the "NAME" slot are 
members of a list, so each value will be appended.

For examples, look inside org.biojava.bio.program.formats, and if you 
are brave look at the deffinition of AnnotationType.setProperty() and 
the things it may defer to.

Matthew

Francois Pepin wrote:

>Hi everyone,
>
>I think that there might be a problem with AnnotationBuilder (parsing
>off Kegg for the curious).
>
>With the following parser:
>      LineSplitParser tvp = new LineSplitParser();
>      tvp.setEndOfRecord("///");
>      tvp.setSplitOffset(12);
>      tvp.setContinueOnEmptyTag(true);
>      tvp.setTrimTag(true);
>      tvp.setTrimValue(false);
>      tvp.setMergeSameTag(true);
>
>The simplest of AnnotationBuilder:
>AnnotationBuilder tvl=new AnnotationBuilder(AnnotationType.ANY);
>
>and the following text (among others):
>NAME        aldehyde dehydrogenase (NAD)
>            CoA-independent aldehyde dehydrogenase
>            m-methylbenzaldehyde dehydrogenase
>            NAD-aldehyde dehydrogenase
>            NAD-dependent 4-hydroxynonenal dehydrogenase
>            NAD-dependent aldehyde dehydrogenase
>            NAD-linked aldehyde dehydrogenase
>            propionaldehyde dehydrogenase
>
>I end up having the following value when printing the Annotation:
>NAME=propionaldehyde dehydrogenase.
>
>Echo() shows that everything is being read properly:
>1  NAME {
>2    aldehyde dehydrogenase (NAD)
>2    CoA-independent aldehyde dehydrogenase
>2    m-methylbenzaldehyde dehydrogenase
>2    NAD-aldehyde dehydrogenase
>2    NAD-dependent 4-hydroxynonenal dehydrogenase
>2    NAD-dependent aldehyde dehydrogenase
>2    NAD-linked aldehyde dehydrogenase
>2    propionaldehyde dehydrogenase
>1  }
>
>Adding the following code (*) in AnnotationBuilder (from line 133), to
>check if the values indeed get to be overwritten.
>
>public void value(TagValueContext ctxt, Object value) {
>    try {
>      Frame top = peek(annotationStack);
>
>*      if (top.annotation.containsProperty(top.tag))
>*          System.out.println("replacing"+
>*top.annotation.getProperty(top.tag)+ " by "+value);
>
>      top.type.setProperty(top.annotation, top.tag, value);
>    } catch (ChangeVetoException cve) {
>      throw new AssertionFailure(cve);
>    }
>  }
>
>This gives us the very interesting output:
>replacing aldehyde dehydrogenase (NAD) by CoA-independent aldehyde
>dehydrogenase replacing CoA-independent aldehyde dehydrogenase by
>m-methylbenzaldehyde dehydrogenase replacing m-methylbenzaldehyde
>dehydrogenase by NAD-aldehyde dehydrogenase replacing NAD-aldehyde
>dehydrogenase by NAD-dependent 4-hydroxynonenal dehydrogenase replacing
>NAD-dependent 4-hydroxynonenal dehydrogenase by NAD-dependent aldehyde
>dehydrogenase replacing NAD-dependent aldehyde dehydrogenase by
>NAD-linked aldehyde dehydrogenase replacing NAD-linked aldehyde
>dehydrogenase by propionaldehyde dehydrogenase
>
>Basically every line gets to be overwritten, so only the last one
>remains at the end.
>
>Any ideas how this could be fixed, or did I do something stupid
>somewhere?
>
>Thanks,
>
>Francois
>
>
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l at biojava.org
>http://biojava.org/mailman/listinfo/biojava-l
>
>  
>