TEXT-77 | String palindrome API

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TEXT-77 | String palindrome API

Amey Jadiye
Hi All,

Though its very trivial to build, by any chance we should have palindrome
method in Apache Commons API ? there is nothing bad having this tool in
our arsenal, preferably in StringUtils ?

https://issues.apache.org/jira/browse/TEXT-77

Regards,
Amey

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Re: TEXT-77 | String palindrome API

Emmanuel Bourg-3
Le 21/06/2017 à 19:17, Amey Jadiye a écrit :

> Though its very trivial to build, by any chance we should have palindrome
> method in Apache Commons API ? there is nothing bad having this tool in
> our arsenal, preferably in StringUtils ?

Like sebb I fail to see the use case for this. Checking palindromes
looks more like an academic exercise to me than a useful feature of a
text oriented library.

Emmanuel Bourg

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Re: TEXT-77 | String palindrome API

garydgregory
On Jun 21, 2017 12:12, "Emmanuel Bourg" <[hidden email]> wrote:

Le 21/06/2017 à 19:17, Amey Jadiye a écrit :

> Though its very trivial to build, by any chance we should have palindrome
> method in Apache Commons API ? there is nothing bad having this tool in
> our arsenal, preferably in StringUtils ?

Like sebb I fail to see the use case for this. Checking palindromes
looks more like an academic exercise to me than a useful feature of a
text oriented library.


+1.

Gary


Emmanuel Bourg

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Re: TEXT-77 | String palindrome API

Rob Tompkins


> On Jun 21, 2017, at 3:22 PM, Gary Gregory <[hidden email]> wrote:
>
> On Jun 21, 2017 12:12, "Emmanuel Bourg" <[hidden email]> wrote:
>
>> Le 21/06/2017 à 19:17, Amey Jadiye a écrit :
>>
>> Though its very trivial to build, by any chance we should have palindrome
>> method in Apache Commons API ? there is nothing bad having this tool in
>> our arsenal, preferably in StringUtils ?
>
> Like sebb I fail to see the use case for this. Checking palindromes
> looks more like an academic exercise to me than a useful feature of a
> text oriented library.

I can see this point fairly clearly, but I also would also be curious to see if openNLP or lucene/solr has such a function. It wouldn't surprise me.

That being said, we should indeed be careful about creating code with no obvious use case. So until we can unearth folks doing palindromic operations let's hold off. I do recall Bruno saying he might have some use cases though.

-Rob

>
> +1.
>
> Gary
>
>
> Emmanuel Bourg
>
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Re: TEXT-77 | String palindrome API

Amey Jadiye
In reply to this post by Emmanuel Bourg-3
Hi,

With little research I found[1] we do have use cases for it like in biology
(I think Bruno might be referring the same fields for its application)

"Palindrome recognition is important in computational biology. Palindromic
structures can frequently be found in proteins and identifying them gives
researchers hints about the structure of nucleic acids. For example, in
nucleic acid secondary structure prediction, one is interested in
complementary palindromes which are considered in the full version."


[1]http://drops.dagstuhl.de/opus/volltexte/2014/4454/pdf/12.pdf

Regards,
Amey

On Jun 22, 2017 12:42 AM, "Emmanuel Bourg" <[hidden email]> wrote:

> Le 21/06/2017 à 19:17, Amey Jadiye a écrit :
>
> > Though its very trivial to build, by any chance we should have palindrome
> > method in Apache Commons API ? there is nothing bad having this tool in
> > our arsenal, preferably in StringUtils ?
>
> Like sebb I fail to see the use case for this. Checking palindromes
> looks more like an academic exercise to me than a useful feature of a
> text oriented library.
>
> Emmanuel Bourg
>
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> To unsubscribe, e-mail: [hidden email]
> For additional commands, e-mail: [hidden email]
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Re: TEXT-77 | String palindrome API

Bruno P. Kinoshita-3
Palindromes (and other algorithms like De Bruijn graphs, lcs) are normally taught in most introductory bioinformatics courses. Not sure how much palindromes are used though. I know use cases for De Bruijn and lcs.

Maybe taking a look at BioJava could help - https://github.com/biojava/biojava-legacy/blob/a909c76131400e6f60048566e33a03f45da2f492/core/src/main/java/org/biojava/bio/molbio/RestrictionEnzyme.java#L291


Palindromes in bioinformatics are not normally used as in text processing. If we had tokenizers, then I think maybe we could identify palindromes in words, in sentences, and in proteins, though not entirely sure.

But would be good to find someone, maybe a bioinformatician, that could confirm if it would be useful, and give a few use cases, for that.

Cheers

Bruno

ps: BioJava is an interesting project, that could maybe someday use [text]. They already use [dbcp], [cli] (transitive from jmol I think), and [math]

________________________________
From: Amey Jadiye <[hidden email]>
To: Commons Developers List <[hidden email]>
Sent: Thursday, 22 June 2017 3:51 PM
Subject: Re: TEXT-77 | String palindrome API



Hi,

With little research I found[1] we do have use cases for it like in biology
(I think Bruno might be referring the same fields for its application)

"Palindrome recognition is important in computational biology. Palindromic
structures can frequently be found in proteins and identifying them gives
researchers hints about the structure of nucleic acids. For example, in
nucleic acid secondary structure prediction, one is interested in
complementary palindromes which are considered in the full version."


[1]http://drops.dagstuhl.de/opus/volltexte/2014/4454/pdf/12.pdf

Regards,
Amey


On Jun 22, 2017 12:42 AM, "Emmanuel Bourg" <[hidden email]> wrote:

> Le 21/06/2017 à 19:17, Amey Jadiye a écrit :
>
> > Though its very trivial to build, by any chance we should have palindrome
> > method in Apache Commons API ? there is nothing bad having this tool in
> > our arsenal, preferably in StringUtils ?
>
> Like sebb I fail to see the use case for this. Checking palindromes
> looks more like an academic exercise to me than a useful feature of a
> text oriented library.
>
> Emmanuel Bourg
>
> ---------------------------------------------------------------------
> To unsubscribe, e-mail: [hidden email]
> For additional commands, e-mail: [hidden email]
>
>

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Re: TEXT-77 | String palindrome API

Emmanuel Bourg-3
Le 22/06/2017 à 06:28, Bruno P. Kinoshita a écrit :

> But would be good to find someone, maybe a bioinformatician, that could confirm if it would be useful, and give a few use cases, for that.

What about waiting for someone with an actual and sensible use case to
request the inclusion of palindrome functions in [text] instead? If we
try to include whatever text processing function we can imagine in
[text], even if they aren't used, we'll end up with an oversized and
bloated API. I think the development should be driven by actual needs
and not by hypothetical usage.

Emmanuel Bourg

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Re: TEXT-77 | String palindrome API

Amey Jadiye
+1 agreed with Emmanuel, better we park/close this issue for now. Its very
trivial and can be pull whenever there will be actual requirement.

Regards,
Amey

On Thu, Jun 22, 2017, 1:50 PM Emmanuel Bourg <[hidden email]> wrote:

> Le 22/06/2017 à 06:28, Bruno P. Kinoshita a écrit :
>
> > But would be good to find someone, maybe a bioinformatician, that could
> confirm if it would be useful, and give a few use cases, for that.
>
> What about waiting for someone with an actual and sensible use case to
> request the inclusion of palindrome functions in [text] instead? If we
> try to include whatever text processing function we can imagine in
> [text], even if they aren't used, we'll end up with an oversized and
> bloated API. I think the development should be driven by actual needs
> and not by hypothetical usage.
>
> Emmanuel Bourg
>
> ---------------------------------------------------------------------
> To unsubscribe, e-mail: [hidden email]
> For additional commands, e-mail: [hidden email]
>
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Re: TEXT-77 | String palindrome API

Rob Tompkins


> On Jun 22, 2017, at 4:38 AM, Amey Jadiye <[hidden email]> wrote:
>
> +1 agreed with Emmanuel, better we park/close this issue for now. Its very
> trivial and can be pull whenever there will be actual requirement.
>
> Regards,
> Amey
>
>> On Thu, Jun 22, 2017, 1:50 PM Emmanuel Bourg <[hidden email]> wrote:
>>
>>> Le 22/06/2017 à 06:28, Bruno P. Kinoshita a écrit :
>>>
>>> But would be good to find someone, maybe a bioinformatician, that could
>> confirm if it would be useful, and give a few use cases, for that.
>>
>> What about waiting for someone with an actual and sensible use case to
>> request the inclusion of palindrome functions in [text] instead? If we
>> try to include whatever text processing function we can imagine in
>> [text], even if they aren't used, we'll end up with an oversized and
>> bloated API. I think the development should be driven by actual needs
>> and not by hypothetical usage.

I think I would take the tactic of searching across Apache code bases to see if such a functionality is written. If it's in two or more different projects then think about bringing it in?

-Rob

>>
>> Emmanuel Bourg
>>
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