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<p class=MsoNormal>Hi,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I’ve encountered problems constructing nested Boolean
expressions in Drools 5.0 using the prefixOr syntax. We’re using
Drools to build a genome annotation system at the Venter Institute.
The following example rule assigns an annotation if there is
a blast hit to a gene GB|AAQ16631.1, or either a blast hit to gene GB|AAQ16631.1,
or to any gene within 500 bases of a gene with an HMM hit to TIGR00905.
I’ve left off some details to focus on how we are structuring the syntax
of our prefixOr and prefixAnd expressions.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>The Drools parser throws errors when it encounters the 2<sup>nd</sup>
“blast_hit” statement in the example below. Our prefixOr and
prefixAnd expressions work as expected when we use similar syntax, at least
until we attempt to use nested or expressions.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal style='text-autospace:none'><b><span style='font-size:10.0pt;
font-family:"Courier New";color:#960000'>rule</span></b><span style='font-size:
10.0pt;font-family:"Courier New";color:black'> </span><span style='font-size:
10.0pt;font-family:"Courier New";color:green'>"2645|lysine decarboxylase
CadA"</span><span style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><b><span style='font-size:10.0pt;
font-family:"Courier New";color:#960000'>when</span></b><span style='font-size:
10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> (</span><b><span
style='font-size:10.0pt;font-family:"Courier New";color:#960000'>or</span></b><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> (</span><b><span
style='font-size:10.0pt;font-family:"Courier New";color:#960000'>and</span></b><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> blast_hit
: BlastHit( hitId==</span><span style='font-size:10.0pt;font-family:"Courier New";
color:green'>'GB|AAQ16631.1'</span><span style='font-size:10.0pt;font-family:
"Courier New";color:black'>)</span><span style='font-size:10.0pt;font-family:
"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> gene1
: Feature( featureId == blast_hit.queryId )</span><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> )</span><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> (</span><b><span
style='font-size:10.0pt;font-family:"Courier New";color:#960000'>or</span></b><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> (</span><b><span
style='font-size:10.0pt;font-family:"Courier New";color:#960000'>and</span></b><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> blast_hit
: BlastHit( hitId==</span><span style='font-size:10.0pt;font-family:"Courier New";
color:green'>'GB|AAQ16631.1'</span><span style='font-size:10.0pt;font-family:
"Courier New";color:black'> )</span><span style='font-size:10.0pt;font-family:
"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> gene1
: Feature( featureId == blast_hit.queryId )</span><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> )</span><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> (</span><b><span
style='font-size:10.0pt;font-family:"Courier New";color:#960000'>and</span></b><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> hmm_hit1
: HmmHit( hitId==</span><span style='font-size:10.0pt;font-family:"Courier New";
color:green'>'TIGR00905'</span><span style='font-size:10.0pt;font-family:"Courier New";
color:black'> )</span><span style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> gene1
: Feature( featureId == hmm_hit1.queryId )</span><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> gene2
: Feature( </span><b><span style='font-size:10.0pt;font-family:"Courier New";
color:#960000'>eval</span></b><span style='font-size:10.0pt;font-family:"Courier New";
color:black'>(gene2.isWithin(gene1, 500)) )</span><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> )</span><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> )</span><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> )</span><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><b><span style='font-size:10.0pt;
font-family:"Courier New";color:#960000'>then</span></b><span style='font-size:
10.0pt;font-family:"Courier New";color:black'> </span><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> Annotation
a = </span><b><span style='font-size:10.0pt;font-family:"Courier New";
color:#960000'>new</span></b><span style='font-size:10.0pt;font-family:"Courier New";
color:black'> Annotation(</span><span style='font-size:10.0pt;font-family:"Courier New";
color:green'>"lysine decarboxylase CadA"</span><span
style='font-size:10.0pt;font-family:"Courier New";color:black'>);<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New";color:black'> gene1.addAnnotation(a);</span><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><b><span style='font-size:10.0pt;
font-family:"Courier New";color:#960000'>end</span></b><span style='font-size:
10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Any suggestions are much appreciated.<o:p></o:p></p>
<p class=MsoNormal>Thanks,<o:p></o:p></p>
<p class=MsoNormal>Nelson<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
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