displaying configuration does not work

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displaying configuration does not work

Pengcheng Yang

Dear InterMiners,

Class SequenceAlteration is an extension of class SequenceFeature. To display SequenceAlteration, I have added the following section to the file webconfig-model.xml. Meanwhile, I also added SequenceFeatureDisplayer and OverlappingFeaturesDisplayer, and removed <class className="org.intermine.model.bio.SequenceFeature">. However, only the primaryIdentifier column of SequenceAlteration class is displayed, which is set by the BioEntity class displaying setting. It seems that the settings for SequenceAlteration class not work at all. The project repository located at: https://github.com/pengchy/fawmine.

Best,

Pengcheng


    <class className="org.intermine.model.bio.SequenceAlteration ">
      <fields>
        <fieldconfig fieldExpr="geneDetail.primaryIdentifier" showInResults="true" showInInlineCollection="false" />
        <fieldconfig fieldExpr="primaryIdentifier"/>
        <fieldconfig fieldExpr="referenceSequence" label="Reference"/>
        <fieldconfig fieldExpr="variantSequence" label="Variation"/>
        <fieldconfig fieldExpr="chromosome.primaryIdentifier"/>
        <fieldconfig fieldExpr="locations.start"/>
        <fieldconfig fieldExpr="positionOnGene"/>
        <fieldconfig fieldExpr="exonicFunction"/>
        <fieldconfig fieldExpr="aAChange" label="AminoAcidChange"/>
      </fields>
    </class>




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Re: displaying configuration does not work

Daniela Butano-2

Dear Pengcheng,

I have seen that you defined the new class SequenceAlteration in the faw-vcf bio-source.

Please, any time you add a new bio-source, remember to call ./gralew clean.

About your question, could you please be more specific? Where do you want to display SequenceAlteration?

Thanks,

Daniela

On 23/02/2020 14:38, Pengcheng Yang wrote:

Dear InterMiners,

Class SequenceAlteration is an extension of class SequenceFeature. To display SequenceAlteration, I have added the following section to the file webconfig-model.xml. Meanwhile, I also added SequenceFeatureDisplayer and OverlappingFeaturesDisplayer, and removed <class className="org.intermine.model.bio.SequenceFeature">. However, only the primaryIdentifier column of SequenceAlteration class is displayed, which is set by the BioEntity class displaying setting. It seems that the settings for SequenceAlteration class not work at all. The project repository located at: https://github.com/pengchy/fawmine.

Best,

Pengcheng


    <class className="org.intermine.model.bio.SequenceAlteration ">
      <fields>
        <fieldconfig fieldExpr="geneDetail.primaryIdentifier" showInResults="true" showInInlineCollection="false" />
        <fieldconfig fieldExpr="primaryIdentifier"/>
        <fieldconfig fieldExpr="referenceSequence" label="Reference"/>
        <fieldconfig fieldExpr="variantSequence" label="Variation"/>
        <fieldconfig fieldExpr="chromosome.primaryIdentifier"/>
        <fieldconfig fieldExpr="locations.start"/>
        <fieldconfig fieldExpr="positionOnGene"/>
        <fieldconfig fieldExpr="exonicFunction"/>
        <fieldconfig fieldExpr="aAChange" label="AminoAcidChange"/>
      </fields>
    </class>




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Re: displaying configuration does not work

Pengcheng Yang

Dear Daniela,

The expected format of SequenceAlteration displaying including the following fields: geneDetail.primaryIdentifier, primaryIdentifier, referenceSequence, variantSequence, locations.start, positionOnGene, exonicFunction, aAChange. Because these fields tell about the position and consequences of the allele. However, the current displaying only contain the primaryIdentifier, the end users hence have to click on each allele to check the detail content in a new window.

Thank you for your always helpful supports!

Pengcheng

On 2020-2-24 19:34, Daniela Butano wrote:

Dear Pengcheng,

I have seen that you defined the new class SequenceAlteration in the faw-vcf bio-source.

Please, any time you add a new bio-source, remember to call ./gralew clean.

About your question, could you please be more specific? Where do you want to display SequenceAlteration?

Thanks,

Daniela

On 23/02/2020 14:38, Pengcheng Yang wrote:

Dear InterMiners,

Class SequenceAlteration is an extension of class SequenceFeature. To display SequenceAlteration, I have added the following section to the file webconfig-model.xml. Meanwhile, I also added SequenceFeatureDisplayer and OverlappingFeaturesDisplayer, and removed <class className="org.intermine.model.bio.SequenceFeature">. However, only the primaryIdentifier column of SequenceAlteration class is displayed, which is set by the BioEntity class displaying setting. It seems that the settings for SequenceAlteration class not work at all. The project repository located at: https://github.com/pengchy/fawmine.

Best,

Pengcheng


    <class className="org.intermine.model.bio.SequenceAlteration ">
      <fields>
        <fieldconfig fieldExpr="geneDetail.primaryIdentifier" showInResults="true" showInInlineCollection="false" />
        <fieldconfig fieldExpr="primaryIdentifier"/>
        <fieldconfig fieldExpr="referenceSequence" label="Reference"/>
        <fieldconfig fieldExpr="variantSequence" label="Variation"/>
        <fieldconfig fieldExpr="chromosome.primaryIdentifier"/>
        <fieldconfig fieldExpr="locations.start"/>
        <fieldconfig fieldExpr="positionOnGene"/>
        <fieldconfig fieldExpr="exonicFunction"/>
        <fieldconfig fieldExpr="aAChange" label="AminoAcidChange"/>
      </fields>
    </class>




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Re: displaying configuration does not work

sergio contrino-2
dear Pengcheng,
we are having some difficulties in understanding your problem. looking
at your fawmine online all seems fine, and in particular we don't see
any allele.
could you explain better what is the issue?
sorry!
thanks
sergio

On 24/02/2020 14:18, Pengcheng Yang wrote:

> Dear Daniela,
>
> The expected format of /SequenceAlteration/ displaying including the
> following fields: /geneDetail.primaryIdentifier/, /primaryIdentifier/,
> /referenceSequence/, /variantSequence/, /locations.start/,
> /positionOnGene/, /exonicFunction/, /aAChange/. Because these fields
> tell about the position and consequences of the allele. However, the
> current displaying only contain the /primaryIdentifier/, the end users
> hence have to click on each allele to check the detail content in a new
> window.
>
> Thank you for your always helpful supports!
>
> Pengcheng
>
> On 2020-2-24 19:34, Daniela Butano wrote:
>>
>> Dear Pengcheng,
>>
>> I have seen that you defined the new class /SequenceAlteration/ in the
>> faw-vcf bio-source.
>>
>> Please, any time you add a new bio-source, remember to call ./gralew
>> clean.
>>
>> About your question, could you please be more specific? Where do you
>> want to display /SequenceAlteration?/
>>
>> Thanks,
>>
>> /Daniela/
>>
>> On 23/02/2020 14:38, Pengcheng Yang wrote:
>>>
>>> Dear InterMiners,
>>>
>>> Class /SequenceAlteration/ is an extension of class
>>> /SequenceFeature/. To display /SequenceAlteration/, I have added the
>>> following section to the file webconfig-model.xml. Meanwhile, I also
>>> added /SequenceFeatureDisplayer/ and /OverlappingFeaturesDisplayer/,
>>> and removed <class
>>> className="org.intermine.model.bio.SequenceFeature">. However, only
>>> the primaryIdentifier column of /SequenceAlteration/ class is
>>> displayed, which is set by the /BioEntity/ class displaying setting.
>>> It seems that the settings for /SequenceAlteration/ class not work at
>>> all. The project repository located at:
>>> https://github.com/pengchy/fawmine.
>>>
>>> Best,
>>>
>>> Pengcheng
>>>
>>>
>>>     <class className="org.intermine.model.bio.SequenceAlteration ">
>>>       <fields>
>>>         <fieldconfig fieldExpr="geneDetail.primaryIdentifier"
>>> showInResults="true" showInInlineCollection="false" />
>>>         <fieldconfig fieldExpr="primaryIdentifier"/>
>>>         <fieldconfig fieldExpr="referenceSequence" label="Reference"/>
>>>         <fieldconfig fieldExpr="variantSequence" label="Variation"/>
>>>         <fieldconfig fieldExpr="chromosome.primaryIdentifier"/>
>>>         <fieldconfig fieldExpr="locations.start"/>
>>>         <fieldconfig fieldExpr="positionOnGene"/>
>>>         <fieldconfig fieldExpr="exonicFunction"/>
>>>         <fieldconfig fieldExpr="aAChange" label="AminoAcidChange"/>
>>>       </fields>
>>>     </class>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
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Re: displaying configuration does not work

Pengcheng Yang

Dear Sergio,

Thank you for your reply. Take this gene for example: http://insectmine.org:8080/fawmine/gene:SFR01273.

Picture [1] listed below is the displayed content, only one column, although I have configured the displayed content in the webconfig-model.xml file:

<class className="org.intermine.model.bio.SequenceAlteration ">
    <fields>
    <fieldconfig fieldExpr="geneDetail.primaryIdentifier"/>
    <fieldconfig fieldExpr="primaryIdentifier"/>
    <fieldconfig fieldExpr="referenceSequence"/>
    <fieldconfig fieldExpr="variantSequence"/>
    <fieldconfig fieldExpr="chromosome.primaryIdentifier "/>
    <fieldconfig fieldExpr="locations.start"/>
    <fieldconfig fieldExpr="positionOnGene"/>
    <fieldconfig fieldExpr="exonicFunction"/>
    <fieldconfig fieldExpr="aAChange"/>
    </fields>
</class>

picture [1]

After manually adding the expected columns, the displaying should be like this:

picture [2]


Thank you!

Best,

Pengcheng

On 2020-2-26 18:32, sergio contrino wrote:
dear Pengcheng,
we are having some difficulties in understanding your problem. looking at your fawmine online all seems fine, and in particular we don't see any allele.
could you explain better what is the issue?
sorry!
thanks
sergio

On 24/02/2020 14:18, Pengcheng Yang wrote:
Dear Daniela,

The expected format of /SequenceAlteration/ displaying including the following fields: /geneDetail.primaryIdentifier/, /primaryIdentifier/, /referenceSequence/, /variantSequence/, /locations.start/, /positionOnGene/, /exonicFunction/, /aAChange/. Because these fields tell about the position and consequences of the allele. However, the current displaying only contain the /primaryIdentifier/, the end users hence have to click on each allele to check the detail content in a new window.

Thank you for your always helpful supports!

Pengcheng

On 2020-2-24 19:34, Daniela Butano wrote:

Dear Pengcheng,

I have seen that you defined the new class /SequenceAlteration/ in the faw-vcf bio-source.

Please, any time you add a new bio-source, remember to call ./gralew clean.

About your question, could you please be more specific? Where do you want to display /SequenceAlteration?/

Thanks,

/Daniela/

On 23/02/2020 14:38, Pengcheng Yang wrote:

Dear InterMiners,

Class /SequenceAlteration/ is an extension of class /SequenceFeature/. To display /SequenceAlteration/, I have added the following section to the file webconfig-model.xml. Meanwhile, I also added /SequenceFeatureDisplayer/ and /OverlappingFeaturesDisplayer/, and removed <class className="org.intermine.model.bio.SequenceFeature">. However, only the primaryIdentifier column of /SequenceAlteration/ class is displayed, which is set by the /BioEntity/ class displaying setting. It seems that the settings for /SequenceAlteration/ class not work at all. The project repository located at: https://github.com/pengchy/fawmine.

Best,

Pengcheng


    <class className="org.intermine.model.bio.SequenceAlteration ">
      <fields>
        <fieldconfig fieldExpr="geneDetail.primaryIdentifier" showInResults="true" showInInlineCollection="false" />
        <fieldconfig fieldExpr="primaryIdentifier"/>
        <fieldconfig fieldExpr="referenceSequence" label="Reference"/>
        <fieldconfig fieldExpr="variantSequence" label="Variation"/>
        <fieldconfig fieldExpr="chromosome.primaryIdentifier"/>
        <fieldconfig fieldExpr="locations.start"/>
        <fieldconfig fieldExpr="positionOnGene"/>
        <fieldconfig fieldExpr="exonicFunction"/>
        <fieldconfig fieldExpr="aAChange" label="AminoAcidChange"/>
      </fields>
    </class>




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Re: displaying configuration does not work

sergio contrino-2
thank you Pengcheng,
i see what you mean now, and it seems that you are doing the right
thing. i suppose you have run the clean before redeploying.
i'll do some test here to check if something has gone wrong. maybe you
could try to use the sequencefeature displayer as illustrated here
https://intermine.readthedocs.io/en/latest/webapp/report-page/report-displayers-examples/
for the moment.
thanks!
sergio


On 26/02/2020 15:24, Pengcheng Yang wrote:

> Dear Sergio,
>
> Thank you for your reply. Take this gene for example:
> http://insectmine.org:8080/fawmine/gene:SFR01273.
>
> Picture [1] listed below is the displayed content, only one column,
> although I have configured the displayed content in the
> webconfig-model.xml file:
>
> <class className="org.intermine.model.bio.SequenceAlteration ">
>      <fields>
>      <fieldconfig fieldExpr="geneDetail.primaryIdentifier"/>
>      <fieldconfig fieldExpr="primaryIdentifier"/>
>      <fieldconfig fieldExpr="referenceSequence"/>
>      <fieldconfig fieldExpr="variantSequence"/>
>      <fieldconfig fieldExpr="chromosome.primaryIdentifier "/>
>      <fieldconfig fieldExpr="locations.start"/>
>      <fieldconfig fieldExpr="positionOnGene"/>
>      <fieldconfig fieldExpr="exonicFunction"/>
>      <fieldconfig fieldExpr="aAChange"/>
>      </fields>
> </class>
>
> picture [1]
>
> After manually adding the expected columns, the displaying should be
> like this:
>
> picture [2]
>
>
> Thank you!
>
> Best,
>
> Pengcheng
>
> On 2020-2-26 18:32, sergio contrino wrote:
>> dear Pengcheng,
>> we are having some difficulties in understanding your problem. looking
>> at your fawmine online all seems fine, and in particular we don't see
>> any allele.
>> could you explain better what is the issue?
>> sorry!
>> thanks
>> sergio
>>
>> On 24/02/2020 14:18, Pengcheng Yang wrote:
>>> Dear Daniela,
>>>
>>> The expected format of /SequenceAlteration/ displaying including the
>>> following fields: /geneDetail.primaryIdentifier/,
>>> /primaryIdentifier/, /referenceSequence/, /variantSequence/,
>>> /locations.start/, /positionOnGene/, /exonicFunction/, /aAChange/.
>>> Because these fields tell about the position and consequences of the
>>> allele. However, the current displaying only contain the
>>> /primaryIdentifier/, the end users hence have to click on each allele
>>> to check the detail content in a new window.
>>>
>>> Thank you for your always helpful supports!
>>>
>>> Pengcheng
>>>
>>> On 2020-2-24 19:34, Daniela Butano wrote:
>>>>
>>>> Dear Pengcheng,
>>>>
>>>> I have seen that you defined the new class /SequenceAlteration/ in
>>>> the faw-vcf bio-source.
>>>>
>>>> Please, any time you add a new bio-source, remember to call ./gralew
>>>> clean.
>>>>
>>>> About your question, could you please be more specific? Where do you
>>>> want to display /SequenceAlteration?/
>>>>
>>>> Thanks,
>>>>
>>>> /Daniela/
>>>>
>>>> On 23/02/2020 14:38, Pengcheng Yang wrote:
>>>>>
>>>>> Dear InterMiners,
>>>>>
>>>>> Class /SequenceAlteration/ is an extension of class
>>>>> /SequenceFeature/. To display /SequenceAlteration/, I have added
>>>>> the following section to the file webconfig-model.xml. Meanwhile, I
>>>>> also added /SequenceFeatureDisplayer/ and
>>>>> /OverlappingFeaturesDisplayer/, and removed <class
>>>>> className="org.intermine.model.bio.SequenceFeature">. However, only
>>>>> the primaryIdentifier column of /SequenceAlteration/ class is
>>>>> displayed, which is set by the /BioEntity/ class displaying
>>>>> setting. It seems that the settings for /SequenceAlteration/ class
>>>>> not work at all. The project repository located at:
>>>>> https://github.com/pengchy/fawmine.
>>>>>
>>>>> Best,
>>>>>
>>>>> Pengcheng
>>>>>
>>>>>
>>>>>     <class className="org.intermine.model.bio.SequenceAlteration ">
>>>>>       <fields>
>>>>>         <fieldconfig fieldExpr="geneDetail.primaryIdentifier"
>>>>> showInResults="true" showInInlineCollection="false" />
>>>>>         <fieldconfig fieldExpr="primaryIdentifier"/>
>>>>>         <fieldconfig fieldExpr="referenceSequence" label="Reference"/>
>>>>>         <fieldconfig fieldExpr="variantSequence" label="Variation"/>
>>>>>         <fieldconfig fieldExpr="chromosome.primaryIdentifier"/>
>>>>>         <fieldconfig fieldExpr="locations.start"/>
>>>>>         <fieldconfig fieldExpr="positionOnGene"/>
>>>>>         <fieldconfig fieldExpr="exonicFunction"/>
>>>>>         <fieldconfig fieldExpr="aAChange" label="AminoAcidChange"/>
>>>>>       </fields>
>>>>>     </class>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email]
>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>>
>>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
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Re: displaying configuration does not work

Pengcheng Yang

Hi Sergio,

Thank you for your help and always support. It turned out that some errors in the configuration for SequenceAlteration. And the problem has been solved by the following configuration setting.

  <class className="org.intermine.model.bio.SequenceAlteration">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="referenceSequence"/>
      <fieldconfig fieldExpr="variantSequence"/>
      <fieldconfig fieldExpr="chromosome.primaryIdentifier"/>
      <fieldconfig fieldExpr="locations.start"/>
      <fieldconfig fieldExpr="positionOnGene"/>
      <fieldconfig fieldExpr="exonicFunction"/>
      <fieldconfig fieldExpr="aAChange"/>
    </fields>
  </class>

Thank you and best,

Pengcheng


On 2020-2-27 1:32, sergio contrino wrote:
thank you Pengcheng,
i see what you mean now, and it seems that you are doing the right thing. i suppose you have run the clean before redeploying.
i'll do some test here to check if something has gone wrong. maybe you could try to use the sequencefeature displayer as illustrated here
https://intermine.readthedocs.io/en/latest/webapp/report-page/report-displayers-examples/
for the moment.
thanks!
sergio


On 26/02/2020 15:24, Pengcheng Yang wrote:
Dear Sergio,

Thank you for your reply. Take this gene for example: http://insectmine.org:8080/fawmine/gene:SFR01273.

Picture [1] listed below is the displayed content, only one column, although I have configured the displayed content in the webconfig-model.xml file:

<class className="org.intermine.model.bio.SequenceAlteration ">
     <fields>
     <fieldconfig fieldExpr="geneDetail.primaryIdentifier"/>
     <fieldconfig fieldExpr="primaryIdentifier"/>
     <fieldconfig fieldExpr="referenceSequence"/>
     <fieldconfig fieldExpr="variantSequence"/>
     <fieldconfig fieldExpr="chromosome.primaryIdentifier "/>
     <fieldconfig fieldExpr="locations.start"/>
     <fieldconfig fieldExpr="positionOnGene"/>
     <fieldconfig fieldExpr="exonicFunction"/>
     <fieldconfig fieldExpr="aAChange"/>
     </fields>
</class>

picture [1]

After manually adding the expected columns, the displaying should be like this:

picture [2]


Thank you!

Best,

Pengcheng

On 2020-2-26 18:32, sergio contrino wrote:
dear Pengcheng,
we are having some difficulties in understanding your problem. looking at your fawmine online all seems fine, and in particular we don't see any allele.
could you explain better what is the issue?
sorry!
thanks
sergio

On 24/02/2020 14:18, Pengcheng Yang wrote:
Dear Daniela,

The expected format of /SequenceAlteration/ displaying including the following fields: /geneDetail.primaryIdentifier/, /primaryIdentifier/, /referenceSequence/, /variantSequence/, /locations.start/, /positionOnGene/, /exonicFunction/, /aAChange/. Because these fields tell about the position and consequences of the allele. However, the current displaying only contain the /primaryIdentifier/, the end users hence have to click on each allele to check the detail content in a new window.

Thank you for your always helpful supports!

Pengcheng

On 2020-2-24 19:34, Daniela Butano wrote:

Dear Pengcheng,

I have seen that you defined the new class /SequenceAlteration/ in the faw-vcf bio-source.

Please, any time you add a new bio-source, remember to call ./gralew clean.

About your question, could you please be more specific? Where do you want to display /SequenceAlteration?/

Thanks,

/Daniela/

On 23/02/2020 14:38, Pengcheng Yang wrote:

Dear InterMiners,

Class /SequenceAlteration/ is an extension of class /SequenceFeature/. To display /SequenceAlteration/, I have added the following section to the file webconfig-model.xml. Meanwhile, I also added /SequenceFeatureDisplayer/ and /OverlappingFeaturesDisplayer/, and removed <class className="org.intermine.model.bio.SequenceFeature">. However, only the primaryIdentifier column of /SequenceAlteration/ class is displayed, which is set by the /BioEntity/ class displaying setting. It seems that the settings for /SequenceAlteration/ class not work at all. The project repository located at: https://github.com/pengchy/fawmine.

Best,

Pengcheng


    <class className="org.intermine.model.bio.SequenceAlteration ">
      <fields>
        <fieldconfig fieldExpr="geneDetail.primaryIdentifier" showInResults="true" showInInlineCollection="false" />
        <fieldconfig fieldExpr="primaryIdentifier"/>
        <fieldconfig fieldExpr="referenceSequence" label="Reference"/>
        <fieldconfig fieldExpr="variantSequence" label="Variation"/>
        <fieldconfig fieldExpr="chromosome.primaryIdentifier"/>
        <fieldconfig fieldExpr="locations.start"/>
        <fieldconfig fieldExpr="positionOnGene"/>
        <fieldconfig fieldExpr="exonicFunction"/>
        <fieldconfig fieldExpr="aAChange" label="AminoAcidChange"/>
      </fields>
    </class>




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