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<ol
style="margin-left: 0.3159in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in; font-family: Calibri; font-size: 11pt;">
<p style="margin: 0in; font-family: Calibri; font-size: 11pt;">Hi
guys,<br>
<br>
</p>
<p style="margin: 0in; font-family: Calibri; font-size: 11pt;">A
couple of days back I was having some problem with hibernate exception
but that exception got resolved and the reference to that email is:<span
style=""> </span><a
href="http://old.nabble.com/Hibernate-Exception-when-persisting-some-richsequence-object-to-biosql-schema-to27299245.html">http://old.nabble.com/Hibernate-Exception-when-persisting-some-richsequence-object-to-biosql-schema-to27299245.html</a></p>
<p style="margin: 0in; font-family: Calibri; font-size: 11pt;">On
Richard<span style=""> </span>suggestion in above link<span style="">
</span>I am able to resolve some of<span style=""> </span>issues
but then, I got stuck in to some other error with hibernate and then
decided to investigate the matter and below are some facts and
information which I found and I guess it is going to affect all of us.<br>
</p>
</ol>
<ol>
<li><span style="font-family: Calibri; font-size: 11pt;">The "</span><span
style="font-weight: bold; font-family: Calibri; font-size: 11pt;">Reference</span><span
style="font-family: Calibri; font-size: 11pt;">" table in bioSql
schema have </span><span
style="font-weight: bold; font-family: Calibri; font-size: 11pt;">unique
constraint</span><span style="font-family: Calibri; font-size: 11pt;">
on "</span><span
style="font-weight: bold; font-family: Calibri; font-size: 11pt;">dbxref_id</span><span
style="font-family: Calibri; font-size: 11pt;">" column (CONSTRAINT
reference_dbxref_id_key UNIQUE (dbxref_id)). Which mean only one entry
in reference table can use on dbxref_id. </span></li>
</ol>
<ol
style="margin-left: 0.3159in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in; font-family: Calibri; font-size: 11pt;">
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;">This
Works wells but in cases when you have little variation in value of
following column<span style="font-weight: bold;"> "location", "title",
"authors"</span> and all these variation refers to same <span
style="font-weight: bold;">PUBMED_ID</span>. Then we can't persist or
create a richsequence object .</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"> Now
when you tie <span style="font-weight: bold;">RichObjectFactory</span>
to a<span style=""> </span>active hibernate session then the class<span
style=""> </span><span style="font-weight: bold;">"BioSqlRichObjectBuilder</span>"
have method called "<span style="font-weight: bold;">buildObject(Class
clazz, List paramsList)</span> " which is responsible<span style=""> </span>for
<span style="font-weight: bold;">looking up details of object</span>
in the database and if it find one then it will return that object,
else it will try to persist the new object into the database.</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;">But
problem is with below part of that method:</p>
<p
style="margin: 0in 0in 0in 0.75in; font-style: italic; font-family: Calibri; font-size: 11pt;">…..LineNumber:
114</p>
<p
style="margin: 0in 0in 0in 0.75in; font-style: italic; font-family: Calibri; font-size: 11pt;">else
if (SimpleDocRef.class.isAssignableFrom(clazz))</p>
<p
style="margin: 0in 0in 0in 0.75in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>{<span style=""> </span> queryType =
"DocRef";</p>
<p
style="margin: 0in 0in 0in 0.75in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span> // convert List constructor to String
representation for query</p>
<p
style="margin: 0in 0in 0in 0.75in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span> ourParamsList.set(0,
DocRefAuthor.Tools.generateAuthorString((List)ourParamsList.get(0),
true));</p>
<p
style="margin: 0in 0in 0in 0.75in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span> if (ourParamsList.size()<3) {</p>
<p
style="margin: 0in 0in 0in 0.75in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span> <span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;"> queryText
= "from DocRef as cr where cr.authors = ? and cr.location = ? and
cr.title is null";</span></p>
<p
style="margin: 0in 0in 0in 0.75in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span> } else {</p>
<p
style="margin: 0in 0in 0in 0.75in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span> <span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;"> queryText
= "from DocRef as cr where cr.authors = ? and cr.location = ? and
cr.title = ?";</span></p>
<p
style="margin: 0in 0in 0in 0.75in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span> }<span style=""> </span></p>
<p
style="margin: 0in 0in 0in 0.75in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>}</p>
<p
style="margin: 0in 0in 0in 0.75in; font-style: italic; font-family: Calibri; font-size: 11pt;">..LineNubmer:
123</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;">Now
when hibernate search the database, it won't find any other record in <span
style="font-weight: bold;">"reference" </span>table because those two
record are different in string comparison, so it will return a new
object back to <span style="font-weight: bold;">"GenbankFormat" </span>to
following piece of code</p>
<p
style="margin: 0in 0in 0in 1.125in; font-style: italic; font-family: Calibri; font-size: 11pt;">….LineNumber:
447</p>
<p
style="margin: 0in 0in 0in 1.125in; font-style: italic; font-family: Calibri; font-size: 11pt;">else
{</p>
<p
style="margin: 0in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>try {</p>
<p
style="margin: 0in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;"><span
style=""> </span>CrossRef
cr = (CrossRef)RichObjectFactory.getObject(SimpleCrossRef.class,new
Object[]{dbname, raccession, new Integer(0)});</span></p>
<p
style="margin: 0in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>RankedCrossRef
rcr = new SimpleRankedCrossRef(cr, ++rcrossrefCount);</p>
<p
style="margin: 0in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>rlistener.getCurrentFeature().addRankedCrossRef(rcr);</p>
<p
style="margin: 0in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>} catch
(ChangeVetoException e) {</p>
<p
style="margin: 0in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>throw new
ParseException(e+", accession:"+accession);</p>
<p
style="margin: 0in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>}</p>
<p
style="margin: 0in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>}</p>
<p
style="margin: 0in 0in 0in 0.375in; font-style: italic; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>…..LineNumber:455</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;">Then
we will add that object to rlistener. And move to next part of genbank
record and then biojava search for a new crossref in database and it
will try to persist the old one it get a hibernate exception regarding
violation of<span style=""> </span><span style="font-weight: bold;">"unique
constraint on dbxref_id"</span> column. </p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"> </p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;">The
only way to get these record in database is:</p>
<ul
style="margin-left: 0.75in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in;"
type="disc">
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">The very easy solution
and the way I did it for testing my theory is Change the bioSql schema
so that it can allow many to one on relation between "reference" and
"dbxref" table.<span style=""> </span>Which even make sense because
one paper can have many different variation of naming, and this change
allow us to store that info too. But this is something BioSql people
have decide and I don't know how to approach them. </span></li>
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">Second solution is
slightly difficult to implement, is to change the way </span><span
style="font-weight: bold; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>"BioSqlRichObjectBuilder.buildObject(Class clazz,List
paramsList)" </span><span
style="font-family: Calibri; font-size: 11pt;"><span style=""> </span>make
decision about weather a particular DocRef already exist in database or
not. I am mean testing all possible string variations of authors,
location, title of the docRef which we are searching. Which does have
many complications and may slow down process of creating a richsequence
object when link RichObjectFactory with a active hibernate session.</span></li>
</ul>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"> </p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style="font-weight: bold;">Example:</span>Below is a sample of what i
have in my local biosql schema which has modification suggested by me.
(dbxref_id column have Pubmed_id , I replaced the local dbxref_id which
was present on this table in my database with pubmed_id stored in
"dbxref" table, for easy reference with outside world) </p>
<div style="direction: ltr;">
<table valign="top"
style="border: 1pt solid rgb(163, 163, 163); direction: ltr; border-collapse: collapse; margin-left: 0.3333in;"
border="1" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.9875in;">
<p
style="margin: 0in; font-weight: bold; font-family: Calibri; font-size: 10pt; color: black;">Reference_id</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8805in;">
<p
style="margin: 0in; font-weight: bold; font-family: Calibri; font-size: 10pt; color: black;">Dbxref_id
</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 1.6388in;">
<p
style="margin: 0in; font-weight: bold; font-family: Calibri; font-size: 10pt; color: black;">Location</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 3.1756in;">
<p
style="margin: 0in; font-weight: bold; font-family: Calibri; font-size: 10pt; color: black;">Title</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 7.4631in;">
<p
style="margin: 0in; font-weight: bold; font-family: Calibri; font-size: 10pt; color: black;">Authors</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8958in;">
<p
style="margin: 0in; font-weight: bold; font-family: Calibri; font-size: 10pt; color: black;">crc</p>
</td>
</tr>
<tr>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.9875in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">216</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8805in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">18554304</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 1.6388in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">FEMS
Microbiol. Ecol. 66 <span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">(3THEMATIC
ISSUE: GUT MICROBIOLOGY), 528-536 (2008)</span></p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 3.1756in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Isolation
of lactate-utilizing butyrate-producing bacteria from human feces and
in vivo administration of Anaerostipes caccae strain L2 and
galacto-oligosaccharides in a rat model</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 7.4631in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Sato,T.,
Matsumoto,K., Okumura,T., Yokoi,W., Naito,E., Yoshida,Y., Nomoto,K.,
Ito,M. and Sawada,H.</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8958in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">9E940E01F4BE3CD0</p>
</td>
</tr>
<tr>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.9875in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">230</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8805in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">18554304</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 1.6388in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">FEMS
Microbiol. Ecol. 66 (3), 528-536 (2008)</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 3.1756in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Isolation
of lactate-utilizing butyrate-producing bacteria from human feces and
in vivo administration of Anaerostipes caccae strain L2 and
galacto-oligosaccharides in a rat model</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 7.4631in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Sato,T.,
Matsumoto,K., Okumura,T., Yokoi,W., Naito,E., Yoshida,Y., Nomoto,K.,
Ito,M. and Sawada,H.</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8958in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">D3BC0C17F3F786C9</p>
</td>
</tr>
<tr>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.9875in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">415</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8805in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">16790744</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 1.6388in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Infect.
Immun. 74 (7), 3715-3726 (2006)</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 3.1756in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;"><span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">Intrastrain
Heterogeneity</span> of the mgpB <span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">Gene
in Mycoplasma</span> genitalium Is <span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">Extensive
In Vitro</span> and In V<span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">ivo
and Suggests that Variation Is Generated via Recombination with
Repetitive Chromosomal Sequences</span></p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 7.4631in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Iverson-Cabral,S.L.,
Astete,S.G., Cohen,C.R., Rocha,E.P. and Totten,P.A.</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8958in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">60AEDFA0CEEACC38</p>
</td>
</tr>
<tr>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.9875in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">969</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8805in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">16790744</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 1.6388in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Infect.
Immun. 74 (7), 3715-3726 (2006)</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 3.1756in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;"><span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">Intrastrain
heterogeneity of the mgpB gene in mycoplasma genitalium is extensive in
vitro and in vivo and suggests that variation is generated via
recombination with repetitive chromosomal sequences</span></p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 7.4631in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Iverson-Cabral,S.L.,
Astete,S.G., Cohen,C.R., Rocha,E.P. and Totten,P.A.</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8958in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">4B1232999F6E8130</p>
</td>
</tr>
<tr>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.9875in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">929</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8805in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">8688087</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 1.6388in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Science
273 (5278), 1058-1073 (1996)</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 3.1756in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Complete
genome sequence of the methanogenic archaeon, Methanococcus jannaschii</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 7.4631in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Bult,C.J.,
White,O., Olsen,G.J., Zhou,L., Fleischmann,R.D., Sutton,G.G.,
Blake,J.A., FitzGerald,L.M., Clayton,R.A., Gocayne,J.D.,
Kerlavage,A.R., Dougherty,B.A., <span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">Tomb,J.-F</span>.,
Adams,M.D., Reich,C.I., Overbeek,R., Kirkness,E.F., Weinstock,K.G.,
Merrick,J.M., Glodek,A., Scott,J.L., Geoghagen,N.S.M., Weidman,J.F.,
Fuhrmann,J.L., Presley,E.A., Nguyen,D., Utterback,T.R., Kelley,J.M.,
Peterson,J.D., Sadow,P.W., Hanna,M.C., Cotton,M.D., Hurst,M.A.,
Roberts,K.M., Kaine,B.P., Borodovsky,M., Klenk,H.-P., Fraser,C.M.,
Smith,H.O., Woese,C.R. and Venter,J.C.</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8958in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">3E79B40DD2AAA2B7</p>
</td>
</tr>
<tr>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.9875in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">932</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8805in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">8688087</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 1.6388in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Science
273 (5278), 1058-1073 (1996)</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 3.1756in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Complete
genome sequence of the methanogenic archaeon, Methanococcus jannaschii</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 7.4631in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Bult,C.J.,
White,O., Olsen,G.J., Zhou,L., Fleischmann,R.D., Sutton,G.G.,
Blake,J.A., FitzGerald,L.M., Clayton,R.A., Gocayne,J.D.,
Kerlavage,A.R., Dougherty,B.A., <span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">Tomb,J.</span>,
Adams,M.D., Reich,C.I., Overbeek,R., Kirkness,E.F., Weinstock,K.G.,
Merrick,J.M., Glodek,A., Scott,J.D., Geoghagen,N.S., Weidman,J.F.,
Fuhrmann,J.L., Nguyen,D.T., Utterback,T., Kelley,J.M., Peterson,J.D.,
Sadow,P.W., Hanna,M.C., Cotton,M.D., Hurst,M.A., Roberts,K.M.,
Kaine,B.B., Borodovsky,M., Klenk,H.P., Fraser,C.M., Smith,H.O.,
Woese,C.R. and Venter,J.C.</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8958in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">094EB3384F8D6DE8</p>
</td>
</tr>
<tr>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.9875in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">1426</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8805in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">10684935</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 1.6388in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Nucleic
Acids Res. 28 (6), 1397-1406 (2000)</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 3.1756in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Genome
sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 7.4631in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;"><span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">Read,T.D.,</span>
Brunham,R.C., Shen,C., Gill,S.R., Heidelberg,J.F., White,O., <span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">Hickey,E.K.</span>,
<span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">Peterson,J.,
Umayam,L.A., Utterback,T.</span>, Berry,K., Bass,S., Linher,K.,
Weidman,J., Khouri,H., Craven,B., Bowman,C., Dodson,R., Gwinn,M.,
Nelson,W., DeBoy,R., Kolonay,J., McClarty,G., Salzberg,S.L., Eisen,J.
and Fraser,C.M.</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8958in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">357648D8FD8C6C8A</p>
</td>
</tr>
<tr>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.9875in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">1481</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8805in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">10684935</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 1.6388in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Nucleic
Acids Res. 28 (6), 1397-1406 (2000)</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 3.1756in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Genome
sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 7.4631in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;"><span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">Read,T.</span>,
Brunham,R., Shen,C., Gill,S., Heidelberg,J., White,O.,<span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">
Hickey,E.,</span> <span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">Peterson,J.,
Utterback,T.</span>, Berry,K., Bass,S., Linher,K., Weidman,J.,
Khouri,H., Craven,B., Bowman,C., Dodson,R., Gwinn,M., Nelson,W.,
DeBoy,R., Kolonay,J., McClarty,G., Salzberg,S., Eisen,J. and Fraser,C.</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8958in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">115411EB2DEE5654</p>
</td>
</tr>
<tr>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.9875in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">1497</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8805in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">14689165</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 1.6388in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Arch.
Microbiol. 181 (2), 144-154 (2004)</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 3.1756in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">The
effect of FITA mutations on the symbiotic properties of Sinorhizobium
fredii varies in a chromosomal-background-dependent manner</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 7.4631in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Vinardell,J.M.,
Lopez-Baena,F.J., Hidalgo,A., Ollero,F.J., Bellogin,R., <span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">del
Rosario</span> Espuny,M., Temprano,F., Romero,F., Krishnan,H.B.,
Pueppke,S.G. and Ruiz-Sainz,J.E.</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8958in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">4D5D376EECCD186B</p>
</td>
</tr>
<tr>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.9875in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">1501</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8805in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">14689165</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 1.6388in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Arch.
Microbiol. 181 (2), 144-154 (2004)</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 3.1756in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">The
effect of FITA mutations on the symbiotic properties of Sinorhizobium
fredii varies in a chromosomal-background-dependent manner</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 7.4631in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Vinardell,J.M.,
Lopez-Baena,F.J., Hidalgo,A., Ollero,F.J., Bellogin,R.,<span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">
Del Rosario</span> Espuny,M., Temprano,F., Romero,F., Krishnan,H.B.,
Pueppke,S.G. and Ruiz-Sainz,J.E.</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8958in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">4D57954EECDED66B</p>
</td>
</tr>
<tr>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.9875in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">1556</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8805in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">18060065</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 1.6388in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">PLoS
ONE 2 (12), E1271 (2007)</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 3.1756in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Analysis
of the <span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">Neurotoxin</span>
<span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">Complex
Genes</span> in Clostridium botulinum A1-A4 and B1 Strains: BoNT/A3,
/Ba4 and /B1 Clusters Are Located within Plasmids</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 7.4631in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Smith,T.J.,
Hill,K.K., Foley,B.T., Detter,J.C., Munk,A.C., Bruce,D.C.,
Doggett,N.A., Smith,L.A., Marks,J.D., Xie,G. and Brettin,T.S.</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8958in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">698688FB6DB95247</p>
</td>
</tr>
<tr>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.9875in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">1559</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8805in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black; text-align: right;">18060065</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 1.6388in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">PLoS
ONE 2 (12), E1271 (2007)</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 3.1756in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Analysis
of the<span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">
neurotoxin</span> <span
style="background: yellow none repeat scroll 0% 0%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">complex
genes</span> in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3,
/Ba4 and /B1 clusters are located within plasmids</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 7.4631in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">Smith,T.J.,
Hill,K.K., Foley,B.T., Detter,J.C., Munk,C.A., Bruce,D.C.,
Doggett,N.A., Smith,L.A., Marks,J.D., Xie,G. and Brettin,T.S.</p>
</td>
<td
style="border: 1pt solid rgb(163, 163, 163); padding: 4pt; vertical-align: top; width: 0.8958in;">
<p
style="margin: 0in; font-family: Calibri; font-size: 11pt; color: black;">E25E1BA99DB18F3D</p>
</td>
</tr>
</tbody>
</table>
</div>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"> </p>
</ol>
<ol start="2">
<li><span style="font-family: Calibri; font-size: 11pt;">The second
kind of error which I got was :<b>
org.hibernate.PropertyValueException: not-null property references a
null or transient value: Location.feature</b></span></li>
</ol>
<ol
style="margin-left: 0.3159in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in; font-family: Calibri; font-size: 11pt;">
<ul
style="margin-left: 0.375in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in;"
type="circle">
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">Which means in
richsequence object some feature have location object which have its
feature set to null.</span></li>
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-weight: bold; font-family: Calibri; font-size: 11pt;">My
Observation: </span></li>
<ul
style="margin-left: 0.375in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in;"
type="disc">
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">Usually occur when you
try to persist a richsequence object to database, and occur to those
features which have <b>CompoundRichLocation </b>usually "joins" and
"complement" in cds region of a genbank record</span></li>
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">After catching the
hibernate exception I went through all the features and either biojava
or hibernate<span style=""> </span>changed the object type of a
CompoundRichLocation<span style=""> </span>to SimpleRichLocation and
set the feature variable to null.</span></li>
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">Below is the screen
shot of one of my tests</span></li>
<ul
style="margin-left: 0.375in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in;"
type="square">
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-weight: bold; font-family: Calibri; font-size: 11pt;">Settings
before trying to persits the richsequence object to database</span></li>
</ul>
</ul>
</ul>
<p
style="margin: 0in 0in 0in 1.125in; font-weight: bold; font-family: Calibri; font-size: 11pt;"> </p>
<p style="margin: 0in 0in 0in 1.125in;"><img
src="cid:part1.06040203.09060607@gmail.com" alt=""></p>
<ul
style="margin-left: 1.125in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in;"
type="square">
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"> </li>
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-weight: bold; font-family: Calibri; font-size: 11pt;">After
trying to persits the richsequence object to database and got in
hibernate exception catch</span></li>
</ul>
<p
style="margin: 0in 0in 0in 1.125in; font-weight: bold; font-family: Calibri; font-size: 11pt;"> </p>
<ul
style="margin-left: 1.125in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in;"
type="square">
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle; font-size: 11pt;"><img
src="cid:part2.00060602.02040909@gmail.com" alt=""></li>
</ul>
<p
style="margin: 0in 0in 0in 0.375in; font-weight: bold; font-family: Calibri; font-size: 11pt;"> </p>
<ul
style="margin-left: 0.375in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in;"
type="circle">
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-weight: bold; font-family: Calibri; font-size: 11pt;">So
my question is why is this happening and how to stop or how to get
these record into database, I have no clue why is this happening.</span></li>
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">Some extra information
to make things more clear to you guys.</span></li>
<ul
style="margin-left: 0.375in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in;"
type="disc">
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">Below are some Locus
line from genbank record for which I know the error of location, I mean
the cds region causing error, and array index in richsequence.feature
arrayList object. </span></li>
<ol
style="margin-left: 0.375in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in; font-family: Calibri; font-size: 11pt;"
type="1">
<li value="1"
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">LOCUS<span style="">
</span>AE001439<span style=""> </span>1643831 bp<span
style=""> </span>DNA<span style=""> </span>circular BCT
19-JAN-2006</span></li>
<ul
style="margin-left: 0.375in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in;"
type="disc">
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">richSequence.feature
Index : 2540 and line number in the genbank record : 22115</span></li>
</ul>
</ol>
<ol
style="margin-left: 0.375in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in; font-family: Calibri; font-size: 11pt;"
type="1">
<li value="2"
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">LOCUS<span style="">
</span>CP001189<span style=""> </span>3887492 bp<span
style=""> </span>DNA<span style=""> </span>circular BCT
16-OCT-2008</span></li>
<ul
style="margin-left: 0.375in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in;"
type="disc">
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">richSequence.feature
Index : 127 and line number in the genbank record : 2137</span></li>
</ul>
</ol>
<ol
style="margin-left: 0.375in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in; font-family: Calibri; font-size: 11pt;"
type="1">
<li value="3"
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">LOCUS<span style="">
</span>CP001292<span style=""> </span>328635 bp<span
style=""> </span>DNA<span style=""> </span>circular BCT
17-DEC-2008</span></li>
<ul
style="margin-left: 0.375in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in;"
type="disc">
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">richSequence.feature
Index : 389 and line number in the genbank record : 3632</span></li>
</ul>
</ol>
<ol
style="margin-left: 0.375in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in; font-family: Calibri; font-size: 11pt;"
type="1">
<li value="4"
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">LOCUS<span style="">
</span>AM279694<span style=""> </span>238517 bp<span
style=""> </span>DNA<span style=""> </span>linear<span
style=""> </span>BCT 23-OCT-2008</span></li>
<ul
style="margin-left: 0.375in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in;"
type="disc">
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">richSequence.feature
Index : 47 and line number in the genbank record : 4841</span></li>
</ul>
</ol>
<ol
style="margin-left: 0.375in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in; font-family: Calibri; font-size: 11pt;"
type="1">
<li value="5"
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">LOCUS<span style="">
</span>CR931663<span style=""> </span>18517 bp<span
style=""> </span>DNA<span style=""> </span>linear<span
style=""> </span>BCT 18-SEP-2008</span></li>
<ul
style="margin-left: 0.375in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in;"
type="disc">
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">richSequence.feature
Index : 45 and line number in the genbank record : 442</span></li>
</ul>
</ol>
</ul>
</ul>
<ul
style="margin-left: 0.375in; direction: ltr; unicode-bidi: embed; margin-top: 0in; margin-bottom: 0in;"
type="circle">
<li
style="margin-top: 0pt; margin-bottom: 0pt; vertical-align: middle;"><span
style="font-family: Calibri; font-size: 11pt;">The complete exception
msg :</span></li>
</ul>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;">org.hibernate.PropertyValueException:
not-null property references a null or transient value: Location.feature</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Nullability.checkNullability(Nullability.java:72)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:290)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Cascade.cascade(Cascade.java:130)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(AbstractSaveEventListener.java:456)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:334)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.engine.Cascade.cascade(Cascade.java:130)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(AbstractSaveEventListener.java:456)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:334)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.DefaultSaveEventListener.saveWithGeneratedOrRequestedId(DefaultSaveEventListener.java:33)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.DefaultSaveEventListener.performSaveOrUpdate(DefaultSaveEventListener.java:27)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.impl.SessionImpl.fireSave(SessionImpl.java:535)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
org.hibernate.impl.SessionImpl.save(SessionImpl.java:523)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"><span
style=""> </span>at
trashtesting.GenBankLoaderTesting.main(GenBankLoaderTesting.java:78)</p>
<p
style="margin: 0in 0in 0in 0.375in; font-family: Calibri; font-size: 11pt;"> </p>
<p
style="margin: 0in 0in 0in 0.75in; font-family: Calibri; font-size: 11pt;"> </p>
</ol>
</body>
</html>