From daniel.quest at gmail.com  Tue Oct  2 23:31:46 2012
From: daniel.quest at gmail.com (Daniel Quest)
Date: Tue, 2 Oct 2012 22:31:46 -0500
Subject: [Biojava-l] maven + genbank parser
Message-ID: <CAHm=Cq7AHaR4bRjccVVY1diWBL6jbV227Qh+QRN4BB_rHF1GDw@mail.gmail.com>

Is there an example project that uses maven to access the genbank parser?
 I am confused if biojava3 has genbank support.  If I want to use an
earlier version along the lines of the cookbook does it exist in a maven
repo?

Thanks
Dan

From andreas at sdsc.edu  Wed Oct  3 01:09:28 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 2 Oct 2012 22:09:28 -0700
Subject: [Biojava-l] maven + genbank parser
In-Reply-To: <CAHm=Cq7AHaR4bRjccVVY1diWBL6jbV227Qh+QRN4BB_rHF1GDw@mail.gmail.com>
References: <CAHm=Cq7AHaR4bRjccVVY1diWBL6jbV227Qh+QRN4BB_rHF1GDw@mail.gmail.com>
Message-ID: <CALthepxwzDJeaViDyU8hjPNQWRQuWXhTpQ7KwH_MLVXn-Ra8bA@mail.gmail.com>

Hi Daniel,

both the 1.8 as well as the 3.0 series are available via maven builds.
You have to configure the biojava specific repo

<repositories>
		...
		<repository>
			<id>biojava-maven-repo</id>
			<name>BioJava repository</name>
			<url>http://www.biojava.org/download/maven/</url>			
		</repository>
	</repositories>

Andreas

On Tue, Oct 2, 2012 at 8:31 PM, Daniel Quest <daniel.quest at gmail.com> wrote:
> Is there an example project that uses maven to access the genbank parser?
>  I am confused if biojava3 has genbank support.  If I want to use an
> earlier version along the lines of the cookbook does it exist in a maven
> repo?
>
> Thanks
> Dan
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

From andreas at sdsc.edu  Mon Oct  8 18:43:43 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 8 Oct 2012 15:43:43 -0700
Subject: [Biojava-l] InstabilityIndex
In-Reply-To: <1349723178.65392.YahooMailNeo@web190604.mail.sg3.yahoo.com>
References: <1349723178.65392.YahooMailNeo@web190604.mail.sg3.yahoo.com>
Message-ID: <CALthepyv+wTAk563YjqoUuY_umw-PHqfFU45GWSPGNwwywTE0g@mail.gmail.com>

Hi Subrata,

Please don't mail me directly, but send your questions to the list.
Chances are that somebody there can help you best.

Ah Fu, do you have any thoughts on this?

Thanks,

Andreas




On Mon, Oct 8, 2012 at 12:06 PM, subrata sinha
<subratasinha2006 at yahoo.co.in> wrote:
> Dear Sir,
>
> I was testing the getInstabilityIndex() method of
> org.biojava3.aaproperties.PeptideProperties class.
>
> I am trying to find InstabilityIndex for very short segment of peptide, as
> short as two. But I am getting some surprising result in negative.Then i
> found that the method perhaps giving -ve result for ambiguous characters. So
> how to handle a situation if my protein sequence contains ambiguous
> characters
>
> Input Sequence            Instability Index
>
> GTDG                      -13.725
> VDVR                      -30.075
>
> How i analyse the above situation.
>
> Kindly help me.
>
>
> With Regards
>
> Subrata Sinha
> Assistant Professor
> Centre for Bioinformatics Studies
> Dibrugarh University

From darnells at dnastar.com  Tue Oct  9 13:32:36 2012
From: darnells at dnastar.com (Steve Darnell)
Date: Tue, 9 Oct 2012 17:32:36 +0000
Subject: [Biojava-l] InstabilityIndex
In-Reply-To: <CALthepyv+wTAk563YjqoUuY_umw-PHqfFU45GWSPGNwwywTE0g@mail.gmail.com>
References: <1349723178.65392.YahooMailNeo@web190604.mail.sg3.yahoo.com>
	<CALthepyv+wTAk563YjqoUuY_umw-PHqfFU45GWSPGNwwywTE0g@mail.gmail.com>
Message-ID: <DFF89F3308438B4291689BA4BDD65D055961034C@MS1.dnastar.com>

@Subrata, The class does not handle characters other than the standard 20 amino acids. We substitute BJOUXZ with DLKCAE and live with the approximation.

@Ah Fu, In the past we have used average values for B (D or N), J (L or I), and Z (E or Q), and a dummy substitution for X (G or A). Our U and O substitutions just map to the closest natural amino acid. It would be nice if real values existed for selenocysteine and pyrrolysine, but I haven't a clue if they do.

@Andreas, I would suggest that a general policy that all protein sequence analyses support the 6 non-standard letter would be a good thing. A nice ideal, but who has the time? :)

Regards,
Steve

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic
Sent: Monday, October 08, 2012 5:44 PM
To: subrata sinha
Cc: Chuan Hock Koh; biojava-l at biojava.org
Subject: Re: [Biojava-l] InstabilityIndex

Hi Subrata,

Please don't mail me directly, but send your questions to the list.
Chances are that somebody there can help you best.

Ah Fu, do you have any thoughts on this?

Thanks,

Andreas




On Mon, Oct 8, 2012 at 12:06 PM, subrata sinha <subratasinha2006 at yahoo.co.in> wrote:
> Dear Sir,
>
> I was testing the getInstabilityIndex() method of 
> org.biojava3.aaproperties.PeptideProperties class.
>
> I am trying to find InstabilityIndex for very short segment of 
> peptide, as short as two. But I am getting some surprising result in 
> negative.Then i found that the method perhaps giving -ve result for 
> ambiguous characters. So how to handle a situation if my protein 
> sequence contains ambiguous characters
>
> Input Sequence            Instability Index
>
> GTDG                      -13.725
> VDVR                      -30.075
>
> How i analyse the above situation.
>
> Kindly help me.
>
>
> With Regards
>
> Subrata Sinha
> Assistant Professor
> Centre for Bioinformatics Studies
> Dibrugarh University
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l


From hlapp at drycafe.net  Wed Oct 10 16:31:04 2012
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 10 Oct 2012 16:31:04 -0400
Subject: [Biojava-l] Fwd: [Announce] Call for Proposals for Doc Sprint
	Summit v2.0
References: <CAEkQO62TQA7sge4ChRwO6HR6j42pvt-KfAcj_mEt3VfMmwsEOQ@mail.gmail.com>
Message-ID: <CA82E0D3-9336-4A93-8324-2EE80B0ECA9D@drycafe.net>

If you've been a Google Summer of Code mentor this year or last year, you will have already seen this. I wanted to make sure everybody is aware, and this may provide the opportunity for the kind of concerted effort that could finally get a BioPerl, Biopython, Bioruby, or Biojava (or a combined??) off the ground.

	-hilmar

Begin forwarded message:

From: Carol Smith <carols at google.com>
Subject: [GSoC Mentors] [Announce] Call for Proposals for Doc Sprint Summit v2.0
Date: October 10, 2012 2:44:50 PM EDT
To: Google Summer of Code Mentors List <google-summer-of-code-mentors-list at googlegroups.com>
Cc: adam at flossmanuals.net

Dear GSoC mentors and org admins, 

Google Summer of Code in collaboration with Aspiration and FLOSS Manuals is hosting a "Doc Sprint Camp" at Google's Mountain View headquarters (California) Dec 3 - 7, 2012.

The 2012 Doc Camp will feature:

1) An unconference on free software documentation topics - facilitated by Aspiration

2) 2-5 Book Sprints to produce books on free softwares - facilitated by FLOSS Manuals

Building on the success of the 2011 GSoC Doc Camp we are proud to bring you the 2012 GSoC Doc Camp. Like the previous event the 2012 GSoC Doc Camp is a place for free software communities to meet, create a book for their project, attract new people to their efforts, and share their documentation experiences. The camp aims to improve free documentation materials and skills in free software projects and individuals and help form the identity of the emergent free documentation sector.

Individuals and projects can apply. Food and accommodation for all individuals will be provided and travel support (full or partial) can also be applied for.

Be a part of this exciting event ? propose a Book Sprint on your favorite free software or come and help others write a book on their favorite project. Guaranteed to be a lot of fun, productive, and a fantastic place to advance your documentation efforts and experiences.

For more information or to register to take part, please see https://sites.google.com/site/docsprintsummitv2/. 

Please note proposals are due by October 26, so get yours in ASAP!

Cheers,
Carol Smith, Allen Gunn, Adam Hyde

-- 
You received this message because you are subscribed to the Google Groups "Google Summer of Code Mentors List" group.
To post to this group, send email to google-summer-of-code-mentors-list at googlegroups.com.
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For more options, visit this group at http://groups.google.com/group/google-summer-of-code-mentors-list?hl=en.

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================





-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From andreas at sdsc.edu  Wed Oct 10 22:17:45 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 10 Oct 2012 19:17:45 -0700
Subject: [Biojava-l] InstabilityIndex
In-Reply-To: <DFF89F3308438B4291689BA4BDD65D055961034C@MS1.dnastar.com>
References: <1349723178.65392.YahooMailNeo@web190604.mail.sg3.yahoo.com>
	<CALthepyv+wTAk563YjqoUuY_umw-PHqfFU45GWSPGNwwywTE0g@mail.gmail.com>
	<DFF89F3308438B4291689BA4BDD65D055961034C@MS1.dnastar.com>
Message-ID: <CALthepxHjaKZQL3CDMZkVddy=MbGDo0yshqLvVxDAidLpwHY+g@mail.gmail.com>

Thanks, good comments, Steve.

I agree we should make it a policy from now on to support 6
non-standard letters for anything protein related... About your time
comment - that's part of the idea of moving the development to git..
Ideally,  it should be easier for everybody who is concerned to patch
and share patches...

Andreas


On Tue, Oct 9, 2012 at 10:32 AM, Steve Darnell <darnells at dnastar.com> wrote:
> @Subrata, The class does not handle characters other than the standard 20 amino acids. We substitute BJOUXZ with DLKCAE and live with the approximation.
>
> @Ah Fu, In the past we have used average values for B (D or N), J (L or I), and Z (E or Q), and a dummy substitution for X (G or A). Our U and O substitutions just map to the closest natural amino acid. It would be nice if real values existed for selenocysteine and pyrrolysine, but I haven't a clue if they do.
>
> @Andreas, I would suggest that a general policy that all protein sequence analyses support the 6 non-standard letter would be a good thing. A nice ideal, but who has the time? :)
>
> Regards,
> Steve
>
> -----Original Message-----
> From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic
> Sent: Monday, October 08, 2012 5:44 PM
> To: subrata sinha
> Cc: Chuan Hock Koh; biojava-l at biojava.org
> Subject: Re: [Biojava-l] InstabilityIndex
>
> Hi Subrata,
>
> Please don't mail me directly, but send your questions to the list.
> Chances are that somebody there can help you best.
>
> Ah Fu, do you have any thoughts on this?
>
> Thanks,
>
> Andreas
>
>
>
>
> On Mon, Oct 8, 2012 at 12:06 PM, subrata sinha <subratasinha2006 at yahoo.co.in> wrote:
>> Dear Sir,
>>
>> I was testing the getInstabilityIndex() method of
>> org.biojava3.aaproperties.PeptideProperties class.
>>
>> I am trying to find InstabilityIndex for very short segment of
>> peptide, as short as two. But I am getting some surprising result in
>> negative.Then i found that the method perhaps giving -ve result for
>> ambiguous characters. So how to handle a situation if my protein
>> sequence contains ambiguous characters
>>
>> Input Sequence            Instability Index
>>
>> GTDG                      -13.725
>> VDVR                      -30.075
>>
>> How i analyse the above situation.
>>
>> Kindly help me.
>>
>>
>> With Regards
>>
>> Subrata Sinha
>> Assistant Professor
>> Centre for Bioinformatics Studies
>> Dibrugarh University
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l


From andreas.prlic at gmail.com  Thu Oct 11 14:32:30 2012
From: andreas.prlic at gmail.com (Andreas Prlic)
Date: Thu, 11 Oct 2012 11:32:30 -0700
Subject: [Biojava-l] Biojava Dependency on Forester
In-Reply-To: <CACHsrTvG_LCCZnh=uPdtE7H=5iAB3mZHXR_ZhwDYoyN5GqLgKw@mail.gmail.com>
References: <CACHsrTvG_LCCZnh=uPdtE7H=5iAB3mZHXR_ZhwDYoyN5GqLgKw@mail.gmail.com>
Message-ID: <CALthepzBRXUc2Yi+pnRpdtQ4T+AHXsQ3+0wdsEY_8_33rLZZfQ@mail.gmail.com>

Hi Terry,

Biojava depends on forester version 0.955. There are no plans to get
rid of this dependency, as far as I know. However we can try to
upgrade to a newer version if that helps.

If you are working in a Maven environment and you pull in BioJava that
way, you can add an exclusion to your config. Something like the XML
below. This forces your project to ignore the older forester library
configured in biojava. Is this a suitable workaround for your problem?

Andreas


	<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava3-phylo</artifactId>
			<version>3.0.4</version>
			<exclusions>
				<exclusion>
					<groupId>org</groupId>
					<artifactId>forester</artifactId>
				</exclusion>
			</exclusions>
		</dependency>




On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <tmc46 at cornell.edu> wrote:
> Dear Andreas,
>
> I am the lead developer of the software Tassel.
> http://www.maizegenetics.net/tassel
>
> We currently use Biojava 3.0.  And we are
> wanting to use the latest release of Forester.
> Since Biojava has a dependency on an older
> release of Forester, we are running into conflicts.
> Can you help explain Biojava's dependency on
> Forester?
>
> What version of Forester does Biojava 3.0 require?
> It looks like version 0.955
>
> What version of Forester does Biojava 3.0.4 require?
>
> Does any Biojava jar files include Forester classes?
> Or just references?
>
> Are there plans to remove Biojava's dependency
> on Forester?
>
>
> Thank you,
>
> Terry Casstevens

From andreas.prlic at gmail.com  Thu Oct 11 14:50:10 2012
From: andreas.prlic at gmail.com (Andreas Prlic)
Date: Thu, 11 Oct 2012 11:50:10 -0700
Subject: [Biojava-l] Biojava Dependency on Forester
In-Reply-To: <CACHsrTsteHwDm+wdOtLbHNxwqSRXpQ=JHRwTRRB_b0D4vx7VRQ@mail.gmail.com>
References: <CACHsrTvG_LCCZnh=uPdtE7H=5iAB3mZHXR_ZhwDYoyN5GqLgKw@mail.gmail.com>
	<CALthepzBRXUc2Yi+pnRpdtQ4T+AHXsQ3+0wdsEY_8_33rLZZfQ@mail.gmail.com>
	<CACHsrTsteHwDm+wdOtLbHNxwqSRXpQ=JHRwTRRB_b0D4vx7VRQ@mail.gmail.com>
Message-ID: <CALthepzyPJDJ-jsmn_in5c=1rPho6pTy+oWrBCkou4oBVH0a3Q@mail.gmail.com>

"exclusion" means only that the (old) forester.jar that biojava
depends on, will not be included. Instead you could configure your
newer forester dependency in its own <dependency> section. That one
will get used instead.

A

On Thu, Oct 11, 2012 at 11:43 AM, Terry Casstevens <tmc46 at cornell.edu> wrote:
> Hi Andreas,
>
> Thank you for the quick response!
>
> When you say "exclusion", sounds like the
> parts of biojava that uses forester would be excluded?
> I'm not sure, but I think our code uses some of
> the code that would be excluded.
>
> As you probably already know, the latest
> release of Forester is not backwardly
> compatible with Forester version 0.955.
>
> Thank you,
>
> Terry
>
>
> On Thu, Oct 11, 2012 at 2:32 PM, Andreas Prlic <andreas.prlic at gmail.com> wrote:
>> Hi Terry,
>>
>> Biojava depends on forester version 0.955. There are no plans to get
>> rid of this dependency, as far as I know. However we can try to
>> upgrade to a newer version if that helps.
>>
>> If you are working in a Maven environment and you pull in BioJava that
>> way, you can add an exclusion to your config. Something like the XML
>> below. This forces your project to ignore the older forester library
>> configured in biojava. Is this a suitable workaround for your problem?
>>
>> Andreas
>>
>>
>>         <dependency>
>>                         <groupId>org.biojava</groupId>
>>                         <artifactId>biojava3-phylo</artifactId>
>>                         <version>3.0.4</version>
>>                         <exclusions>
>>                                 <exclusion>
>>                                         <groupId>org</groupId>
>>                                         <artifactId>forester</artifactId>
>>                                 </exclusion>
>>                         </exclusions>
>>                 </dependency>
>>
>>
>>
>>
>> On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <tmc46 at cornell.edu> wrote:
>>> Dear Andreas,
>>>
>>> I am the lead developer of the software Tassel.
>>> http://www.maizegenetics.net/tassel
>>>
>>> We currently use Biojava 3.0.  And we are
>>> wanting to use the latest release of Forester.
>>> Since Biojava has a dependency on an older
>>> release of Forester, we are running into conflicts.
>>> Can you help explain Biojava's dependency on
>>> Forester?
>>>
>>> What version of Forester does Biojava 3.0 require?
>>> It looks like version 0.955
>>>
>>> What version of Forester does Biojava 3.0.4 require?
>>>
>>> Does any Biojava jar files include Forester classes?
>>> Or just references?
>>>
>>> Are there plans to remove Biojava's dependency
>>> on Forester?
>>>
>>>
>>> Thank you,
>>>
>>> Terry Casstevens

From HWillis at scripps.edu  Thu Oct 11 14:46:24 2012
From: HWillis at scripps.edu (Scooter Willis)
Date: Thu, 11 Oct 2012 14:46:24 -0400
Subject: [Biojava-l] Biojava Dependency on Forester
Message-ID: <9CA63734-A43D-4BAE-A744-FF292D1EF972@scripps.edu>

If forester has maven repository we can unhook the local depedency. We use forester for NJ and should only be a needed in one model. Let me know the issue/conflict and I can see what I can do to clean up.

Thanks

Scooter

----- Reply message -----
From: "Andreas Prlic" <andreas.prlic at gmail.com>
To: "Terry Casstevens" <tmc46 at cornell.edu>
Cc: "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz" <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>, "biojava-l at biojava.org" <biojava-l at biojava.org>
Subject: [Biojava-l] Biojava Dependency on Forester
Date: Thu, Oct 11, 2012 2:33 pm



Hi Terry,

Biojava depends on forester version 0.955. There are no plans to get
rid of this dependency, as far as I know. However we can try to
upgrade to a newer version if that helps.

If you are working in a Maven environment and you pull in BioJava that
way, you can add an exclusion to your config. Something like the XML
below. This forces your project to ignore the older forester library
configured in biojava. Is this a suitable workaround for your problem?

Andreas


        <dependency>
                        <groupId>org.biojava</groupId>
                        <artifactId>biojava3-phylo</artifactId>
                        <version>3.0.4</version>
                        <exclusions>
                                <exclusion>
                                        <groupId>org</groupId>
                                        <artifactId>forester</artifactId>
                                </exclusion>
                        </exclusions>
                </dependency>




On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <tmc46 at cornell.edu> wrote:
> Dear Andreas,
>
> I am the lead developer of the software Tassel.
> http://www.maizegenetics.net/tassel
>
> We currently use Biojava 3.0.  And we are
> wanting to use the latest release of Forester.
> Since Biojava has a dependency on an older
> release of Forester, we are running into conflicts.
> Can you help explain Biojava's dependency on
> Forester?
>
> What version of Forester does Biojava 3.0 require?
> It looks like version 0.955
>
> What version of Forester does Biojava 3.0.4 require?
>
> Does any Biojava jar files include Forester classes?
> Or just references?
>
> Are there plans to remove Biojava's dependency
> on Forester?
>
>
> Thank you,
>
> Terry Casstevens
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l


From HWillis at scripps.edu  Thu Oct 11 15:50:26 2012
From: HWillis at scripps.edu (Scooter Willis)
Date: Thu, 11 Oct 2012 15:50:26 -0400
Subject: [Biojava-l] Biojava Dependency on Forester
Message-ID: <47E61FED-17CF-40E9-AE76-E44C11BDBB27@scripps.edu>

Andreas

Looks like the alignment code is using the distance matrix from forester and that has changed. Any chance the developer who did the MSA code could get this working with the latest forester code. It is probably a refactoring problem.

Scooter

----- Reply message -----
From: "Terry Casstevens" <tmc46 at cornell.edu>
To: "Scooter Willis" <HWillis at scripps.edu>
Cc: "Andreas Prlic" <andreas.prlic at gmail.com>, "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz" <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>, "biojava-l at biojava.org" <biojava-l at biojava.org>
Subject: [Biojava-l] Biojava Dependency on Forester
Date: Thu, Oct 11, 2012 2:56 pm



Hi Scooter, Andreas,

Thank you again for the responses.

This is one problem we are seeing.  org/forester/phylogenyinference
does not exist in Forester version 1.005.

Exception in thread "main" java.lang.NoClassDefFoundError:
org/forester/phylogenyinference/DistanceMatrix
at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176)
at net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java:306)
at net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java:183)
at net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.addSitesToMutableAlignment(TagsToSNPByAlignmentPlugin.java:417)
at net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.runTagsToSNPByAlignment(TagsToSNPByAlignmentPlugin.java:347)
at net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.performFunction(TagsToSNPByAlignmentPlugin.java:107)
at net.maizegenetics.gbs.pipeline.TerryPipelines.runTagsToSNPByAlignmentPlugin(TerryPipelines.java:36)
at net.maizegenetics.gbs.pipeline.TerryPipelines.main(TerryPipelines.java:41)
Caused by: java.lang.ClassNotFoundException:
org.forester.phylogenyinference.DistanceMatrix
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:356)


Thank you,

Terry


On Thu, Oct 11, 2012 at 2:46 PM, Scooter Willis <HWillis at scripps.edu> wrote:
> If forester has maven repository we can unhook the local depedency. We use
> forester for NJ and should only be a needed in one model. Let me know the
> issue/conflict and I can see what I can do to clean up.
>
> Thanks
>
> Scooter
>
>
> ----- Reply message -----
> From: "Andreas Prlic" <andreas.prlic at gmail.com>
> To: "Terry Casstevens" <tmc46 at cornell.edu>
> Cc: "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz"
> <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>,
> "biojava-l at biojava.org" <biojava-l at biojava.org>
> Subject: [Biojava-l] Biojava Dependency on Forester
> Date: Thu, Oct 11, 2012 2:33 pm
>
>
>
> Hi Terry,
>
> Biojava depends on forester version 0.955. There are no plans to get
> rid of this dependency, as far as I know. However we can try to
> upgrade to a newer version if that helps.
>
> If you are working in a Maven environment and you pull in BioJava that
> way, you can add an exclusion to your config. Something like the XML
> below. This forces your project to ignore the older forester library
> configured in biojava. Is this a suitable workaround for your problem?
>
> Andreas
>
>
>         <dependency>
>                         <groupId>org.biojava</groupId>
>                         <artifactId>biojava3-phylo</artifactId>
>                         <version>3.0.4</version>
>                         <exclusions>
>                                 <exclusion>
>                                         <groupId>org</groupId>
>                                         <artifactId>forester</artifactId>
>                                 </exclusion>
>                         </exclusions>
>                 </dependency>
>
>
>
>
> On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <tmc46 at cornell.edu>
> wrote:
>> Dear Andreas,
>>
>> I am the lead developer of the software Tassel.
>> http://www.maizegenetics.net/tassel
>>
>> We currently use Biojava 3.0.  And we are
>> wanting to use the latest release of Forester.
>> Since Biojava has a dependency on an older
>> release of Forester, we are running into conflicts.
>> Can you help explain Biojava's dependency on
>> Forester?
>>
>> What version of Forester does Biojava 3.0 require?
>> It looks like version 0.955
>>
>> What version of Forester does Biojava 3.0.4 require?
>>
>> Does any Biojava jar files include Forester classes?
>> Or just references?
>>
>> Are there plans to remove Biojava's dependency
>> on Forester?
>>
>>
>> Thank you,
>>
>> Terry Casstevens
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From kohchuanhock at gmail.com  Sun Oct 14 00:54:44 2012
From: kohchuanhock at gmail.com (Chuan Hock Koh)
Date: Sun, 14 Oct 2012 13:54:44 +0900
Subject: [Biojava-l] InstabilityIndex
In-Reply-To: <CALthepxHjaKZQL3CDMZkVddy=MbGDo0yshqLvVxDAidLpwHY+g@mail.gmail.com>
References: <1349723178.65392.YahooMailNeo@web190604.mail.sg3.yahoo.com>
	<CALthepyv+wTAk563YjqoUuY_umw-PHqfFU45GWSPGNwwywTE0g@mail.gmail.com>
	<DFF89F3308438B4291689BA4BDD65D055961034C@MS1.dnastar.com>
	<CALthepxHjaKZQL3CDMZkVddy=MbGDo0yshqLvVxDAidLpwHY+g@mail.gmail.com>
Message-ID: <CA+rQFrV5XQHCEPz8+T9JSj7mF3CioPqUByMOnKxsNOhjLtkhDQ@mail.gmail.com>

Hi Andreas and Steve,

Sorry for the slow response. Currently, I am in the midst of moving from
Singapore to Japan. Busy with settling into the new job, apartment hunting
etc..

So, what is the conclusion for the problem? Do let me know what you guys
like to be done, as clear as possible :)

I will code them whenever I can find time which I believe I should have
some at the end of this month.

Thanks,
Ah Fu


On Thu, Oct 11, 2012 at 11:17 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Thanks, good comments, Steve.
>
> I agree we should make it a policy from now on to support 6
> non-standard letters for anything protein related... About your time
> comment - that's part of the idea of moving the development to git..
> Ideally,  it should be easier for everybody who is concerned to patch
> and share patches...
>
> Andreas
>
>
> On Tue, Oct 9, 2012 at 10:32 AM, Steve Darnell <darnells at dnastar.com>
> wrote:
> > @Subrata, The class does not handle characters other than the standard
> 20 amino acids. We substitute BJOUXZ with DLKCAE and live with the
> approximation.
> >
> > @Ah Fu, In the past we have used average values for B (D or N), J (L or
> I), and Z (E or Q), and a dummy substitution for X (G or A). Our U and O
> substitutions just map to the closest natural amino acid. It would be nice
> if real values existed for selenocysteine and pyrrolysine, but I haven't a
> clue if they do.
> >
> > @Andreas, I would suggest that a general policy that all protein
> sequence analyses support the 6 non-standard letter would be a good thing.
> A nice ideal, but who has the time? :)
> >
> > Regards,
> > Steve
> >
> > -----Original Message-----
> > From: biojava-l-bounces at lists.open-bio.org [mailto:
> biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic
> > Sent: Monday, October 08, 2012 5:44 PM
> > To: subrata sinha
> > Cc: Chuan Hock Koh; biojava-l at biojava.org
> > Subject: Re: [Biojava-l] InstabilityIndex
> >
> > Hi Subrata,
> >
> > Please don't mail me directly, but send your questions to the list.
> > Chances are that somebody there can help you best.
> >
> > Ah Fu, do you have any thoughts on this?
> >
> > Thanks,
> >
> > Andreas
> >
> >
> >
> >
> > On Mon, Oct 8, 2012 at 12:06 PM, subrata sinha <
> subratasinha2006 at yahoo.co.in> wrote:
> >> Dear Sir,
> >>
> >> I was testing the getInstabilityIndex() method of
> >> org.biojava3.aaproperties.PeptideProperties class.
> >>
> >> I am trying to find InstabilityIndex for very short segment of
> >> peptide, as short as two. But I am getting some surprising result in
> >> negative.Then i found that the method perhaps giving -ve result for
> >> ambiguous characters. So how to handle a situation if my protein
> >> sequence contains ambiguous characters
> >>
> >> Input Sequence            Instability Index
> >>
> >> GTDG                      -13.725
> >> VDVR                      -30.075
> >>
> >> How i analyse the above situation.
> >>
> >> Kindly help me.
> >>
> >>
> >> With Regards
> >>
> >> Subrata Sinha
> >> Assistant Professor
> >> Centre for Bioinformatics Studies
> >> Dibrugarh University
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh<http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh/index.html>

From asidhu at biomap.org  Wed Oct 17 01:28:06 2012
From: asidhu at biomap.org (Amandeep Sidhu)
Date: Wed, 17 Oct 2012 13:28:06 +0800
Subject: [Biojava-l] International Symposium on Biomedical Data
	Infrastructure (BDI 2013)
Message-ID: <CAG_VK1TTWFYLunyqEWYhZEX08OUU9pQJno6e08ugmoxvhuK3KQ@mail.gmail.com>

International Symposium on Biomedical Data Infrastructure (BDI 2013)

30 - 31 January 2013

Kuala Lumpur, Malaysia

http://umconference.um.edu.my/BDI2013

Proceedings to be published by Springer

Due to the emerging demands of huge amounts of biomedical data, new and
improved data management capabilities are required for supporting a wide
range of applications. Current Biomedical Databases are independently
administered in geographically distinct locations, lending them almost
ideally to adoption of intelligent data management approaches. As a result
next generation of information infrastructure and data integration
capabilities are needed to ensure increasing infrastructure agility
required for high-throughput biomedical research. The workshop will focus
on research issues, problems and opportunities in Biomedical Data
Infrastructure.

Topics of Interest are:

* Big Biomedical Data and its Management
* Biomedical Data integration and Interoperability
* Next Generation Sequencing Data
* Biomedical Image Analysis
* Medical Informatics and Translational Bioinformatics
* Biomedical Ontologies
* Semantic Web Tools and Techniques for Biomedicine
* Web 2.0 and Web 3.0 Applications in Biomedicine
* Novel architectural models for HPC and cloud computing in Biomedicine
* New parallel / concurrent programming models for High Performance
Biomedical Applications in Cloud
* Biomedical Data Cloud
* Interoperability between different Utility Computing Platforms used for
Biomedicine
* Performance monitoring for biomedical applications in HPC and Cloud
* Biomedical Infrastructure as a Service
* Biomedical Platforms as a Service
* Biomedical Software as a Service
* Scientific workflows in bioinformatics and biomedicine
* Data Mining in Biomedicine
* Computational Systems Biology

Submission Guidelines:

We welcome original submissions that have not been published and that are
not under review by another conference or journal.  Papers should not
exceed 15 pages excluding references in Springer format. Paper should be
submitted through Easy Chair Online Submission System following
instructions on the website (http://umconference.um.edu.my/BDI2013). All
submissions will be evaluated on their originality, technical soundness,
significance, presentation, and interest to the symposium attendees.
Submission implies the willingness of at least one of the authors to
register and present the work associated with the paper submitted. All
submitted papers will be reviewed by symposium's technical program
committee. All accepted papers of registered authors will be included in
the proceedings published by Springer. All accepted papers will be required
to submit a Springer Copyright Form.

Important Dates:

Paper submission:               20 November 2012

Notifications sent to authors:  10 December 2012

Camera-ready papers due:        24 December 2012

Registration due:               10 January 2013

Conference:                     30 - 31 January 2013

Organizing Chairs:

Dr. Amandeep S. Sidhu (Curtin Sarawak Malaysia, Malaysia)
Dr. Sarinder Kaur (University of Malaya, Malaysia)

Steering Committee:

Dr. Dickson Lukose (MIMOS, Malaysia)
Dr. Kanagasabai Rajaraman (Institute for Infocomm Research, Singapore)
Prof. Dr. Meena Kishore Sakharkar (University of Tsukuba, Japan)
Prof. Dr. Jake Chen (Indiana University-Purdue University Indianapolis,
USA)
Prof. Dr. Xiaohua Tony Hu (Drexel University, USA)
Prof. Dr. Jason Tsong-Li Wang (New Jersey Institute of Technology, USA)
Prof. Dr. Carolyn McGregor (Health Informatics Research, Canada)

Please contact BDI 2013 Secretariat through email bdi at biomap.org for any
queries.

From chapman at cs.wisc.edu  Wed Oct 17 21:08:58 2012
From: chapman at cs.wisc.edu (Mark Chapman)
Date: Wed, 17 Oct 2012 20:08:58 -0500
Subject: [Biojava-l] Biojava Dependency on Forester
In-Reply-To: <47E61FED-17CF-40E9-AE76-E44C11BDBB27@scripps.edu>
References: <47E61FED-17CF-40E9-AE76-E44C11BDBB27@scripps.edu>
Message-ID: <507F56AA.3010001@cs.wisc.edu>

biojava3-alignment and biojava3-phylo have both been updated to use the 
latest forester release: 1.005.  The jar file is in our maven 
repository, and changes are committed to the SVN and git repositories.

Enjoy!
Mark


On 10/11/2012 02:50 PM, Scooter Willis wrote:
> Andreas
>
> Looks like the alignment code is using the distance matrix from forester and that has changed. Any chance the developer who did the MSA code could get this working with the latest forester code. It is probably a refactoring problem.
>
> Scooter
>
> ----- Reply message -----
> From: "Terry Casstevens" <tmc46 at cornell.edu>
> To: "Scooter Willis" <HWillis at scripps.edu>
> Cc: "Andreas Prlic" <andreas.prlic at gmail.com>, "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz" <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>, "biojava-l at biojava.org" <biojava-l at biojava.org>
> Subject: [Biojava-l] Biojava Dependency on Forester
> Date: Thu, Oct 11, 2012 2:56 pm
>
>
>
> Hi Scooter, Andreas,
>
> Thank you again for the responses.
>
> This is one problem we are seeing.  org/forester/phylogenyinference
> does not exist in Forester version 1.005.
>
> Exception in thread "main" java.lang.NoClassDefFoundError:
> org/forester/phylogenyinference/DistanceMatrix
> at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176)
> at net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java:306)
> at net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java:183)
> at net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.addSitesToMutableAlignment(TagsToSNPByAlignmentPlugin.java:417)
> at net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.runTagsToSNPByAlignment(TagsToSNPByAlignmentPlugin.java:347)
> at net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.performFunction(TagsToSNPByAlignmentPlugin.java:107)
> at net.maizegenetics.gbs.pipeline.TerryPipelines.runTagsToSNPByAlignmentPlugin(TerryPipelines.java:36)
> at net.maizegenetics.gbs.pipeline.TerryPipelines.main(TerryPipelines.java:41)
> Caused by: java.lang.ClassNotFoundException:
> org.forester.phylogenyinference.DistanceMatrix
> at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
> at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
>
>
> Thank you,
>
> Terry
>
>
> On Thu, Oct 11, 2012 at 2:46 PM, Scooter Willis <HWillis at scripps.edu> wrote:
>> If forester has maven repository we can unhook the local depedency. We use
>> forester for NJ and should only be a needed in one model. Let me know the
>> issue/conflict and I can see what I can do to clean up.
>>
>> Thanks
>>
>> Scooter
>>
>>
>> ----- Reply message -----
>> From: "Andreas Prlic" <andreas.prlic at gmail.com>
>> To: "Terry Casstevens" <tmc46 at cornell.edu>
>> Cc: "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz"
>> <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>,
>> "biojava-l at biojava.org" <biojava-l at biojava.org>
>> Subject: [Biojava-l] Biojava Dependency on Forester
>> Date: Thu, Oct 11, 2012 2:33 pm
>>
>>
>>
>> Hi Terry,
>>
>> Biojava depends on forester version 0.955. There are no plans to get
>> rid of this dependency, as far as I know. However we can try to
>> upgrade to a newer version if that helps.
>>
>> If you are working in a Maven environment and you pull in BioJava that
>> way, you can add an exclusion to your config. Something like the XML
>> below. This forces your project to ignore the older forester library
>> configured in biojava. Is this a suitable workaround for your problem?
>>
>> Andreas
>>
>>
>>          <dependency>
>>                          <groupId>org.biojava</groupId>
>>                          <artifactId>biojava3-phylo</artifactId>
>>                          <version>3.0.4</version>
>>                          <exclusions>
>>                                  <exclusion>
>>                                          <groupId>org</groupId>
>>                                          <artifactId>forester</artifactId>
>>                                  </exclusion>
>>                          </exclusions>
>>                  </dependency>
>>
>>
>>
>>
>> On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <tmc46 at cornell.edu>
>> wrote:
>>> Dear Andreas,
>>>
>>> I am the lead developer of the software Tassel.
>>> http://www.maizegenetics.net/tassel
>>>
>>> We currently use Biojava 3.0.  And we are
>>> wanting to use the latest release of Forester.
>>> Since Biojava has a dependency on an older
>>> release of Forester, we are running into conflicts.
>>> Can you help explain Biojava's dependency on
>>> Forester?
>>>
>>> What version of Forester does Biojava 3.0 require?
>>> It looks like version 0.955
>>>
>>> What version of Forester does Biojava 3.0.4 require?
>>>
>>> Does any Biojava jar files include Forester classes?
>>> Or just references?
>>>
>>> Are there plans to remove Biojava's dependency
>>> on Forester?
>>>
>>>
>>> Thank you,
>>>
>>> Terry Casstevens
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From andreas at sdsc.edu  Wed Oct 17 21:18:31 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 17 Oct 2012 18:18:31 -0700
Subject: [Biojava-l] Biojava Dependency on Forester
In-Reply-To: <507F56AA.3010001@cs.wisc.edu>
References: <47E61FED-17CF-40E9-AE76-E44C11BDBB27@scripps.edu>
	<507F56AA.3010001@cs.wisc.edu>
Message-ID: <CALthepycmnj9bOP04XyAOXthDS+jE=hJ1e5vd6xY-O91UbySPg@mail.gmail.com>

Awesome, Mark, Thanks for fixing this!

Andreas

On Wed, Oct 17, 2012 at 6:08 PM, Mark Chapman <chapman at cs.wisc.edu> wrote:
> biojava3-alignment and biojava3-phylo have both been updated to use the
> latest forester release: 1.005.  The jar file is in our maven repository,
> and changes are committed to the SVN and git repositories.
>
> Enjoy!
> Mark
>
>
>
> On 10/11/2012 02:50 PM, Scooter Willis wrote:
>>
>> Andreas
>>
>> Looks like the alignment code is using the distance matrix from forester
>> and that has changed. Any chance the developer who did the MSA code could
>> get this working with the latest forester code. It is probably a refactoring
>> problem.
>>
>> Scooter
>>
>> ----- Reply message -----
>> From: "Terry Casstevens" <tmc46 at cornell.edu>
>> To: "Scooter Willis" <HWillis at scripps.edu>
>> Cc: "Andreas Prlic" <andreas.prlic at gmail.com>, "Peter Bradbury"
>> <pjb39 at cornell.edu>, "Jeff Glaubitz" <jcg233 at cornell.edu>, "Ed Buckler"
>> <esb33 at cornell.edu>, "biojava-l at biojava.org" <biojava-l at biojava.org>
>> Subject: [Biojava-l] Biojava Dependency on Forester
>> Date: Thu, Oct 11, 2012 2:56 pm
>>
>>
>>
>> Hi Scooter, Andreas,
>>
>> Thank you again for the responses.
>>
>> This is one problem we are seeing.  org/forester/phylogenyinference
>> does not exist in Forester version 1.005.
>>
>> Exception in thread "main" java.lang.NoClassDefFoundError:
>> org/forester/phylogenyinference/DistanceMatrix
>> at
>> org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176)
>> at
>> net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java:306)
>> at
>> net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java:183)
>> at
>> net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.addSitesToMutableAlignment(TagsToSNPByAlignmentPlugin.java:417)
>> at
>> net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.runTagsToSNPByAlignment(TagsToSNPByAlignmentPlugin.java:347)
>> at
>> net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.performFunction(TagsToSNPByAlignmentPlugin.java:107)
>> at
>> net.maizegenetics.gbs.pipeline.TerryPipelines.runTagsToSNPByAlignmentPlugin(TerryPipelines.java:36)
>> at
>> net.maizegenetics.gbs.pipeline.TerryPipelines.main(TerryPipelines.java:41)
>> Caused by: java.lang.ClassNotFoundException:
>> org.forester.phylogenyinference.DistanceMatrix
>> at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
>> at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
>> at java.security.AccessController.doPrivileged(Native Method)
>> at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
>>
>>
>> Thank you,
>>
>> Terry
>>
>>
>> On Thu, Oct 11, 2012 at 2:46 PM, Scooter Willis <HWillis at scripps.edu>
>> wrote:
>>>
>>> If forester has maven repository we can unhook the local depedency. We
>>> use
>>> forester for NJ and should only be a needed in one model. Let me know the
>>> issue/conflict and I can see what I can do to clean up.
>>>
>>> Thanks
>>>
>>> Scooter
>>>
>>>
>>> ----- Reply message -----
>>> From: "Andreas Prlic" <andreas.prlic at gmail.com>
>>> To: "Terry Casstevens" <tmc46 at cornell.edu>
>>> Cc: "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz"
>>> <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>,
>>> "biojava-l at biojava.org" <biojava-l at biojava.org>
>>> Subject: [Biojava-l] Biojava Dependency on Forester
>>> Date: Thu, Oct 11, 2012 2:33 pm
>>>
>>>
>>>
>>> Hi Terry,
>>>
>>> Biojava depends on forester version 0.955. There are no plans to get
>>> rid of this dependency, as far as I know. However we can try to
>>> upgrade to a newer version if that helps.
>>>
>>> If you are working in a Maven environment and you pull in BioJava that
>>> way, you can add an exclusion to your config. Something like the XML
>>> below. This forces your project to ignore the older forester library
>>> configured in biojava. Is this a suitable workaround for your problem?
>>>
>>> Andreas
>>>
>>>
>>>          <dependency>
>>>                          <groupId>org.biojava</groupId>
>>>                          <artifactId>biojava3-phylo</artifactId>
>>>                          <version>3.0.4</version>
>>>                          <exclusions>
>>>                                  <exclusion>
>>>                                          <groupId>org</groupId>
>>>
>>> <artifactId>forester</artifactId>
>>>                                  </exclusion>
>>>                          </exclusions>
>>>                  </dependency>
>>>
>>>
>>>
>>>
>>> On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <tmc46 at cornell.edu>
>>> wrote:
>>>>
>>>> Dear Andreas,
>>>>
>>>> I am the lead developer of the software Tassel.
>>>> http://www.maizegenetics.net/tassel
>>>>
>>>> We currently use Biojava 3.0.  And we are
>>>> wanting to use the latest release of Forester.
>>>> Since Biojava has a dependency on an older
>>>> release of Forester, we are running into conflicts.
>>>> Can you help explain Biojava's dependency on
>>>> Forester?
>>>>
>>>> What version of Forester does Biojava 3.0 require?
>>>> It looks like version 0.955
>>>>
>>>> What version of Forester does Biojava 3.0.4 require?
>>>>
>>>> Does any Biojava jar files include Forester classes?
>>>> Or just references?
>>>>
>>>> Are there plans to remove Biojava's dependency
>>>> on Forester?
>>>>
>>>>
>>>> Thank you,
>>>>
>>>> Terry Casstevens
>>>
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

From HWillis at scripps.edu  Wed Oct 17 21:49:24 2012
From: HWillis at scripps.edu (Scooter Willis)
Date: Wed, 17 Oct 2012 21:49:24 -0400
Subject: [Biojava-l] Biojava Dependency on Forester
In-Reply-To: <CALthepycmnj9bOP04XyAOXthDS+jE=hJ1e5vd6xY-O91UbySPg@mail.gmail.com>
Message-ID: <CCA4D816.1AB7A%hwillis@scripps.edu>

Thanks Mark! Is Forester on maven to avoid external jar file dependency?

On 10/17/12 9:18 PM, "Andreas Prlic" <andreas at sdsc.edu> wrote:

>Awesome, Mark, Thanks for fixing this!
>
>Andreas
>
>On Wed, Oct 17, 2012 at 6:08 PM, Mark Chapman <chapman at cs.wisc.edu> wrote:
>> biojava3-alignment and biojava3-phylo have both been updated to use the
>> latest forester release: 1.005.  The jar file is in our maven
>>repository,
>> and changes are committed to the SVN and git repositories.
>>
>> Enjoy!
>> Mark
>>
>>
>>
>> On 10/11/2012 02:50 PM, Scooter Willis wrote:
>>>
>>> Andreas
>>>
>>> Looks like the alignment code is using the distance matrix from
>>>forester
>>> and that has changed. Any chance the developer who did the MSA code
>>>could
>>> get this working with the latest forester code. It is probably a
>>>refactoring
>>> problem.
>>>
>>> Scooter
>>>
>>> ----- Reply message -----
>>> From: "Terry Casstevens" <tmc46 at cornell.edu>
>>> To: "Scooter Willis" <HWillis at scripps.edu>
>>> Cc: "Andreas Prlic" <andreas.prlic at gmail.com>, "Peter Bradbury"
>>> <pjb39 at cornell.edu>, "Jeff Glaubitz" <jcg233 at cornell.edu>, "Ed Buckler"
>>> <esb33 at cornell.edu>, "biojava-l at biojava.org" <biojava-l at biojava.org>
>>> Subject: [Biojava-l] Biojava Dependency on Forester
>>> Date: Thu, Oct 11, 2012 2:56 pm
>>>
>>>
>>>
>>> Hi Scooter, Andreas,
>>>
>>> Thank you again for the responses.
>>>
>>> This is one problem we are seeing.  org/forester/phylogenyinference
>>> does not exist in Forester version 1.005.
>>>
>>> Exception in thread "main" java.lang.NoClassDefFoundError:
>>> org/forester/phylogenyinference/DistanceMatrix
>>> at
>>> 
>>>org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignment
>>>s.java:176)
>>> at
>>> 
>>>net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java
>>>:306)
>>> at
>>> 
>>>net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java
>>>:183)
>>> at
>>> 
>>>net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.addSitesToMuta
>>>bleAlignment(TagsToSNPByAlignmentPlugin.java:417)
>>> at
>>> 
>>>net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.runTagsToSNPBy
>>>Alignment(TagsToSNPByAlignmentPlugin.java:347)
>>> at
>>> 
>>>net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.performFunctio
>>>n(TagsToSNPByAlignmentPlugin.java:107)
>>> at
>>> 
>>>net.maizegenetics.gbs.pipeline.TerryPipelines.runTagsToSNPByAlignmentPlu
>>>gin(TerryPipelines.java:36)
>>> at
>>> 
>>>net.maizegenetics.gbs.pipeline.TerryPipelines.main(TerryPipelines.java:4
>>>1)
>>> Caused by: java.lang.ClassNotFoundException:
>>> org.forester.phylogenyinference.DistanceMatrix
>>> at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
>>> at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
>>> at java.security.AccessController.doPrivileged(Native Method)
>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
>>>
>>>
>>> Thank you,
>>>
>>> Terry
>>>
>>>
>>> On Thu, Oct 11, 2012 at 2:46 PM, Scooter Willis <HWillis at scripps.edu>
>>> wrote:
>>>>
>>>> If forester has maven repository we can unhook the local depedency. We
>>>> use
>>>> forester for NJ and should only be a needed in one model. Let me know
>>>>the
>>>> issue/conflict and I can see what I can do to clean up.
>>>>
>>>> Thanks
>>>>
>>>> Scooter
>>>>
>>>>
>>>> ----- Reply message -----
>>>> From: "Andreas Prlic" <andreas.prlic at gmail.com>
>>>> To: "Terry Casstevens" <tmc46 at cornell.edu>
>>>> Cc: "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz"
>>>> <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>,
>>>> "biojava-l at biojava.org" <biojava-l at biojava.org>
>>>> Subject: [Biojava-l] Biojava Dependency on Forester
>>>> Date: Thu, Oct 11, 2012 2:33 pm
>>>>
>>>>
>>>>
>>>> Hi Terry,
>>>>
>>>> Biojava depends on forester version 0.955. There are no plans to get
>>>> rid of this dependency, as far as I know. However we can try to
>>>> upgrade to a newer version if that helps.
>>>>
>>>> If you are working in a Maven environment and you pull in BioJava that
>>>> way, you can add an exclusion to your config. Something like the XML
>>>> below. This forces your project to ignore the older forester library
>>>> configured in biojava. Is this a suitable workaround for your problem?
>>>>
>>>> Andreas
>>>>
>>>>
>>>>          <dependency>
>>>>                          <groupId>org.biojava</groupId>
>>>>                          <artifactId>biojava3-phylo</artifactId>
>>>>                          <version>3.0.4</version>
>>>>                          <exclusions>
>>>>                                  <exclusion>
>>>>                                          <groupId>org</groupId>
>>>>
>>>> <artifactId>forester</artifactId>
>>>>                                  </exclusion>
>>>>                          </exclusions>
>>>>                  </dependency>
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <tmc46 at cornell.edu>
>>>> wrote:
>>>>>
>>>>> Dear Andreas,
>>>>>
>>>>> I am the lead developer of the software Tassel.
>>>>> http://www.maizegenetics.net/tassel
>>>>>
>>>>> We currently use Biojava 3.0.  And we are
>>>>> wanting to use the latest release of Forester.
>>>>> Since Biojava has a dependency on an older
>>>>> release of Forester, we are running into conflicts.
>>>>> Can you help explain Biojava's dependency on
>>>>> Forester?
>>>>>
>>>>> What version of Forester does Biojava 3.0 require?
>>>>> It looks like version 0.955
>>>>>
>>>>> What version of Forester does Biojava 3.0.4 require?
>>>>>
>>>>> Does any Biojava jar files include Forester classes?
>>>>> Or just references?
>>>>>
>>>>> Are there plans to remove Biojava's dependency
>>>>> on Forester?
>>>>>
>>>>>
>>>>> Thank you,
>>>>>
>>>>> Terry Casstevens
>>>>
>>>> _______________________________________________
>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>>
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/biojava-l



From pwrose at ucsd.edu  Thu Oct 18 19:24:43 2012
From: pwrose at ucsd.edu (Peter Rose)
Date: Thu, 18 Oct 2012 23:24:43 +0000
Subject: [Biojava-l] [Job] Lead Web Architect - RCSB PDB
Message-ID: <B5E8EA0C57E75444B91F041CD98E10E90BCA2810@XMAIL-MBX-AT1.AD.UCSD.EDU>

Become part of the RCSB Protein Data Bank team. We have an opening for an experienced Lead Web Architect.

A detailed job description and online application form can be found at:
http://jobs.ucsd.edu/bulletin/job.aspx?cat=information&sortby=post&jobnum_in=64091

Qualifications:

* MS Degree in Computer Science or comparable combination of education and experience with considerable focus in Java EE software development.

* Established demonstrated work experience in the role of an architect and developer on medium to large size database-driven web applications using Java EE technology and standards.

* Advanced experience developing the presentation layer of a dynamic, database-driven web application using HTML, CSS, JavaScript, JavaScript Toolkits, Ajax, JSP, XML, Java. Experience resolving browser and cross-platform compatibility issues. Advanced experience with Struts2, Tiles, jQuery.

* Advanced experience with database design, Structured Query Language and RDBMS's such as MySQL. Expertise in web application server administration and configuration such as Tomcat.

* Established expertise in software life cycle methodologies. Experience with build tools such as Maven and Ant, and continuous integration systems such as Cruise Control. Experience with project tracking tools such as Jira.

________________________________________________
Peter Rose, Ph.D.
Scientific Lead
RCSB Protein Data Bank (http://www.rcsb.org)

San Diego Supercomputer Center (SDSC) and
Skaggs School of Pharmacy and Pharmaceutical Sciences
University of California San Diego




From hlapp at drycafe.net  Mon Oct 22 10:52:24 2012
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Mon, 22 Oct 2012 10:52:24 -0400
Subject: [Biojava-l] regex performance in Java
Message-ID: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>

I know that this is really Java language topic, but since parsing biological data formats is to rife with regular expression applications, I'm curious what the experience is among the Biojava people with the use of regular expressions in Java. 

They (at least as in java.util.regex) have been reported to me as performing much slower (by several orders of magnitude) than the regex implementation in Perl, and some simple benchmarking tests seem to bear that out. Even after scrutinizing the benchmark and finding nothing obvious, I'm still skeptical as to why this would be the case - naively I would have assumed that the underlying runtime library is implemented in C in both cases. But perhaps this is not true?

Any experience people have made here speed-wise (or tricks or things not to do for Java regex's) would be appreciated.

	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From andreas at sdsc.edu  Mon Oct 22 16:42:00 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 22 Oct 2012 13:42:00 -0700
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
Message-ID: <CALthepz64964iGpQ55J43hVw_9Gsgx8AfVFsKsKwo4HRToYf_Q@mail.gmail.com>

Hi Hilmar,

I can't say much about performance of java regular expressions, but
isn't it hard to write efficient regular expressions in any language?
There are great tools in the Java world for parsing of XML/JSON and
other standard file types that help avoiding them. I am not sure if
this is a general rule for the wider Java community, but from my
perspective, the use of regular expressions in Java is only limited
and used if nothing else works... Not sure if anybody else has a
different experience?

Andreas



On Mon, Oct 22, 2012 at 7:52 AM, Hilmar Lapp <hlapp at drycafe.net> wrote:
> I know that this is really Java language topic, but since parsing biological data formats is to rife with regular expression applications, I'm curious what the experience is among the Biojava people with the use of regular expressions in Java.
>
> They (at least as in java.util.regex) have been reported to me as performing much slower (by several orders of magnitude) than the regex implementation in Perl, and some simple benchmarking tests seem to bear that out. Even after scrutinizing the benchmark and finding nothing obvious, I'm still skeptical as to why this would be the case - naively I would have assumed that the underlying runtime library is implemented in C in both cases. But perhaps this is not true?
>
> Any experience people have made here speed-wise (or tricks or things not to do for Java regex's) would be appreciated.
>
>         -hilmar
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From to.petr at gmail.com  Mon Oct 22 16:48:02 2012
From: to.petr at gmail.com (P. Troshin)
Date: Mon, 22 Oct 2012 21:48:02 +0100
Subject: [Biojava-l] Fwd:  regex performance in Java
In-Reply-To: <CAAT4F8ndmJLuCuidA5Yt1mVwp1=gLgVgRuXSqd3J0T_sYu00ew@mail.gmail.com>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<CAAT4F8ndmJLuCuidA5Yt1mVwp1=gLgVgRuXSqd3J0T_sYu00ew@mail.gmail.com>
Message-ID: <CAAT4F8mdvuAwBSb1NAARJ_2rEVaK+rWWiQ8MtWZaYXGdgADYeA@mail.gmail.com>

Sorry, I should have written to the list. Also just want to say that I
agree with Andreas, in Java we use regexp if everything else fails
(:-))

Regards,
P.



---------- Forwarded message ----------
From: P. Troshin <to.petr at gmail.com>
Date: 22 October 2012 21:44
Subject: Re: [Biojava-l] regex performance in Java
To: Hilmar Lapp <hlapp at drycafe.net>


Hi Hilmar,

I think this is one of the myths, I do not think there is a
difference. It might have been true long ago, but I do not think this
is still the case. Last time we compared Perl, Python and Java
performance the former was the last with a large margin :-).  However,
I never had to make a direct comparison of regexp. Google for "perl vs
java regexp speed comparison" brings a few links. I had a quick look
at one result only
(http://onlyjob.blogspot.co.uk/2011/03/perl5-python-ruby-php-c-c-lua-tcl.html),
it claimed that Perl regexp is faster than Java. Unfortunately the
author of the test clearly lacked understanding of Java and as a
result the test compared the performance of String concatenation
(which is notoriously bad in Java, as Strings are immutable) rather
than the regexp performance itself. I guess this is an easy mistake to
make though. Hence the advice - if you are doing a lot of String
permutations use the StringBuilder class, not the String itself.
If you have a Java implementation which is lacking I am sure people on
this list will have no problem optimizing it!

Regards,
Peter



On 22 October 2012 15:52, Hilmar Lapp <hlapp at drycafe.net> wrote:
> I know that this is really Java language topic, but since parsing biological data formats is to rife with regular expression applications, I'm curious what the experience is among the Biojava people with the use of regular expressions in Java.
>
> They (at least as in java.util.regex) have been reported to me as performing much slower (by several orders of magnitude) than the regex implementation in Perl, and some simple benchmarking tests seem to bear that out. Even after scrutinizing the benchmark and finding nothing obvious, I'm still skeptical as to why this would be the case - naively I would have assumed that the underlying runtime library is implemented in C in both cases. But perhaps this is not true?
>
> Any experience people have made here speed-wise (or tricks or things not to do for Java regex's) would be appreciated.
>
>         -hilmar
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From tiagoantao at gmail.com  Mon Oct 22 16:53:56 2012
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Mon, 22 Oct 2012 21:53:56 +0100
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <CALthepz64964iGpQ55J43hVw_9Gsgx8AfVFsKsKwo4HRToYf_Q@mail.gmail.com>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<CALthepz64964iGpQ55J43hVw_9Gsgx8AfVFsKsKwo4HRToYf_Q@mail.gmail.com>
Message-ID: <CAA9RGEMmrX2-PQ-u878tj9Xs24VUBAaKZPxmTdiy=--747nJXg@mail.gmail.com>

On Mon, Oct 22, 2012 at 9:42 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> and used if nothing else works... Not sure if anybody else has a
> different experience?

I might be beating a dead horse here, but I agree. I would say that
from an idiomatic perspective Perl uses a lot of regex programming
(Ruby also?), which is less common in most other languages (Java and
Python are my work case). Regexes exist but are not the first option.
That being said, there is a very cool JVM language which has regexes
as first class objects: Clojure. But even in that case, I do not see
lots of idiomatic use of regexes.

Tiago

From daniel.quest at gmail.com  Tue Oct 23 00:51:37 2012
From: daniel.quest at gmail.com (daniel.quest at gmail.com)
Date: Mon, 22 Oct 2012 23:51:37 -0500
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <CAA9RGEMmrX2-PQ-u878tj9Xs24VUBAaKZPxmTdiy=--747nJXg@mail.gmail.com>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<CALthepz64964iGpQ55J43hVw_9Gsgx8AfVFsKsKwo4HRToYf_Q@mail.gmail.com>
	<CAA9RGEMmrX2-PQ-u878tj9Xs24VUBAaKZPxmTdiy=--747nJXg@mail.gmail.com>
Message-ID: <B9B6FF20-971C-4986-BA71-5475C44C6015@gmail.com>

Wow!  This could open a huge flame war.  Let me just make a couple of quick points about performance.

Perl is implemented in C/C++, It is interpreted, and Java runs bytecode on top of the JVM.  The Venders of JVMs probably write the bytecode instruction set in C/assembly.  Java itself, at least at this point is most likely written in Java.  The speed of Java is greatly influenced by the underlying JVM and how well the JVM instruction set maps to the hardware.  The algorithm being implemented and the version of Java also have a great impact on performance.  Conventional wisdom is that Fortran is the best performing language in widespread use with interpreted languages such as Python, Ruby, and Perl being 3-8 times slower.  This website shows Java having about a ten percent overhead relative to C:  http://shootout.alioth.debian.org/

I have personally noticed superior performance of Perl's Regex parsing capabilities over Python. I have never noticed a difference between Perl and Java that was so extreme that I would choose to implement something in Perl over Java in a production setting.  Java is a language with such deep library support that it makes most every language look like a second class citizen in comparison (notable exceptions: C, C++, and JavaScript)

Something else interesting: http://swtch.com/~rsc/regexp/regexp1.html

Finally, be very cautious of benchmarks.  It is very very hard to do benchmarking well.
Dan 
Sent from my iPhone

On Oct 22, 2012, at 3:53 PM, Tiago Ant?o <tiagoantao at gmail.com> wrote:

> On Mon, Oct 22, 2012 at 9:42 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> and used if nothing else works... Not sure if anybody else has a
>> different experience?
> 
> I might be beating a dead horse here, but I agree. I would say that
> from an idiomatic perspective Perl uses a lot of regex programming
> (Ruby also?), which is less common in most other languages (Java and
> Python are my work case). Regexes exist but are not the first option.
> That being said, there is a very cool JVM language which has regexes
> as first class objects: Clojure. But even in that case, I do not see
> lots of idiomatic use of regexes.
> 
> Tiago
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From khalil.elmazouari at gmail.com  Tue Oct 23 12:48:32 2012
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Tue, 23 Oct 2012 18:48:32 +0200
Subject: [Biojava-l] Biojava-l Digest, Vol 117, Issue 10
In-Reply-To: <mailman.1.1350921602.23329.biojava-l@lists.open-bio.org>
References: <mailman.1.1350921602.23329.biojava-l@lists.open-bio.org>
Message-ID: <99D2DB4A-DD8B-4473-BE04-2834ECF5457E@gmail.com>

Hi Hilmar,

I used regex a lot in perl and java... I was also skeptical about the regex in java when I start using them. 

from my own experience, I can tell you the following:
it's MUCH more easy to write regex in perl than in java.
java regex require more optimisation: working regex and optimal regex are two different things
in java, Patterns must be compiled first. So, if you iterate through a large number of strings you want to match, compile your pattern outside the loop
if you use regex in large iteration, avoid using methods from java.lang.String that use regex: String.replaceFirst, String.replaceAll, String.matches.... your pattern will be compiled each time
Avoid applying regex to large string. If possible, try to limit the matches to the places where the pattern is .. methods like indexOf, lastIndexOf, split ... from java.lang.String are very useful in this regards.
It's more easy to get the matching group in java than in perl
test first with editors like : RegExhibit or your IDE regex plugin.
finally, I recommend the Java Regular Expressions book from Mehran Habibi (http://www.amazon.com/Java-Regular-Expressions-Taming-java-util-regex/dp/1590591070)

If your regex are well optimised, you will not notice any difference between perl/java. 

If you need to use regex in complex algorithm or software in combination with java/biojava, don't hesitate, java regex are excellent. If you just need regex in small script go for perl

Best

khalil 



On 22 Oct 2012, at 18:00, biojava-l-request at lists.open-bio.org wrote:

> Send Biojava-l mailing list submissions to
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> 
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> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Biojava-l digest..."
> 
> 
> Today's Topics:
> 
>   1. regex performance in Java (Hilmar Lapp)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 22 Oct 2012 10:52:24 -0400
> From: Hilmar Lapp <hlapp at drycafe.net>
> Subject: [Biojava-l] regex performance in Java
> To: BioJava <biojava-l at biojava.org>
> Message-ID: <1B62BC3E-B005-4484-AE66-0B8F407E4756 at drycafe.net>
> Content-Type: text/plain; charset=us-ascii
> 
> I know that this is really Java language topic, but since parsing biological data formats is to rife with regular expression applications, I'm curious what the experience is among the Biojava people with the use of regular expressions in Java. 
> 
> They (at least as in java.util.regex) have been reported to me as performing much slower (by several orders of magnitude) than the regex implementation in Perl, and some simple benchmarking tests seem to bear that out. Even after scrutinizing the benchmark and finding nothing obvious, I'm still skeptical as to why this would be the case - naively I would have assumed that the underlying runtime library is implemented in C in both cases. But perhaps this is not true?
> 
> Any experience people have made here speed-wise (or tricks or things not to do for Java regex's) would be appreciated.
> 
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 
> End of Biojava-l Digest, Vol 117, Issue 10
> ******************************************





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From hlapp at drycafe.net  Wed Oct 24 12:47:27 2012
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 24 Oct 2012 12:47:27 -0400
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <874nllo4fx.fsf@newcastle.ac.uk>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<874nllo4fx.fsf@newcastle.ac.uk>
Message-ID: <4F9982AE-FA76-41BF-BF1B-58B7889F03AB@drycafe.net>

Hi everyone, 

Thanks for all your responses. Indeed I know that the Java regex API isn't an enjoyable one to program with, and if the underlying task were about writing something from scratch, I'd be all for avoiding regex's too if the same thing could be achieved by string comparison. 

However, and of course I failed to say that initially, the task from which this query is originating is about converting a Perl script to Java (not because Perl is somehow bad, but because those Perl scripts have shown to be an obstacle to easy cross-platform installation of the - mostly Java - software they are a part of). That doesn't mean one couldn't in the course also rewrite the code that uses regular expressions to one that doesn't, but I also think it wise not to introduce multiple variables as a source of error at once.

Some of the responses would be best answered by looking at the expressions and the code that uses them, so here are the two "benchmark" scripts.

Java: https://gist.github.com/3940931
Perl: https://gist.github.com/3940780

I'm also copying Dongye Meng here, who is a CS student at UNC working with us on the project - if anyone has further wisdom to share about how to reduce the performance gap between the two versions, he'd surely appreciate.

	-hilmar

On Oct 23, 2012, at 6:42 AM, Phillip Lord wrote:

> Hilmar Lapp <hlapp at drycafe.net> writes:
>> They (at least as in java.util.regex) have been reported to me as
>> performing much slower (by several orders of magnitude) than the regex
>> implementation in Perl, and some simple benchmarking tests seem to
>> bear that out. Even after scrutinizing the benchmark and finding
>> nothing obvious, I'm still skeptical as to why this would be the case
>> - naively I would have assumed that the underlying runtime library is
>> implemented in C in both cases. But perhaps this is not true?
> 
> 
> Well, the difference is that Perl is perl, while Java is not; it all
> depends on the JVM, and libraries also. A quick shuftie at
> the source for the open-jdk libraries suggests that the regexp searching
> is done in Java -- it's not just a drop through to C. Always the problem
> with performance optimisation on Java -- you are only optimising for one
> situation. It might be interesting to see how much variation there is
> between JVMs. 
> 
> Like others, I would only use regexp as a last resort in Java anyway;
> compared to Perl, writing the code is painful. Still, I guess that you
> know this!
> 
> Phil

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From to.petr at gmail.com  Wed Oct 24 13:59:19 2012
From: to.petr at gmail.com (P. Troshin)
Date: Wed, 24 Oct 2012 18:59:19 +0100
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <4F9982AE-FA76-41BF-BF1B-58B7889F03AB@drycafe.net>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<874nllo4fx.fsf@newcastle.ac.uk>
	<4F9982AE-FA76-41BF-BF1B-58B7889F03AB@drycafe.net>
Message-ID: <CAAT4F8=St=OseUtdgY_ZbU4-226cXoyQBKmxdeZW6u+h8sq84A@mail.gmail.com>

Hi Hilmar,

You have not mentions the version of JVM you are using, but it appears
that there is a massive difference in timing on my machine.
Here is the timing of the run on Windows 7 (pro 64 bit) with Oracle
JVM (64 bit) v. 1.7.0_02.

# of Iteration: 1t
Time: 1.711E-6 seconds

# of Iteration: 10
Time: 1.711E-6 seconds

# of Iteration: 100
Time: 2.567E-6 seconds

# of Iteration: 1000
Time: 1.2403E-5 seconds

# of Iteration: 10000
Time: 1.44143E-4 seconds

# of Iteration: 100000
Time: 0.001369138 seconds

I have not changed the code at all.
I have 3 year old laptop with Intel Core Duo P8600, 2.4 Ghz CPU. So
nothing special.
I cannot tell whether this is slow or not as you did not publish the
timings for Perl. Could you please do so.

It looks to me that you might just need to update/replace your JVM. I
will be happy to look at the code in a bit more details if this result
is still slower than Perl.

Thanks,
Peter



On 24 October 2012 17:47, Hilmar Lapp <hlapp at drycafe.net> wrote:
> Hi everyone,
>
> Thanks for all your responses. Indeed I know that the Java regex API isn't an enjoyable one to program with, and if the underlying task were about writing something from scratch, I'd be all for avoiding regex's too if the same thing could be achieved by string comparison.
>
> However, and of course I failed to say that initially, the task from which this query is originating is about converting a Perl script to Java (not because Perl is somehow bad, but because those Perl scripts have shown to be an obstacle to easy cross-platform installation of the - mostly Java - software they are a part of). That doesn't mean one couldn't in the course also rewrite the code that uses regular expressions to one that doesn't, but I also think it wise not to introduce multiple variables as a source of error at once.
>
> Some of the responses would be best answered by looking at the expressions and the code that uses them, so here are the two "benchmark" scripts.
>
> Java: https://gist.github.com/3940931
> Perl: https://gist.github.com/3940780
>
> I'm also copying Dongye Meng here, who is a CS student at UNC working with us on the project - if anyone has further wisdom to share about how to reduce the performance gap between the two versions, he'd surely appreciate.
>
>         -hilmar
>
> On Oct 23, 2012, at 6:42 AM, Phillip Lord wrote:
>
>> Hilmar Lapp <hlapp at drycafe.net> writes:
>>> They (at least as in java.util.regex) have been reported to me as
>>> performing much slower (by several orders of magnitude) than the regex
>>> implementation in Perl, and some simple benchmarking tests seem to
>>> bear that out. Even after scrutinizing the benchmark and finding
>>> nothing obvious, I'm still skeptical as to why this would be the case
>>> - naively I would have assumed that the underlying runtime library is
>>> implemented in C in both cases. But perhaps this is not true?
>>
>>
>> Well, the difference is that Perl is perl, while Java is not; it all
>> depends on the JVM, and libraries also. A quick shuftie at
>> the source for the open-jdk libraries suggests that the regexp searching
>> is done in Java -- it's not just a drop through to C. Always the problem
>> with performance optimisation on Java -- you are only optimising for one
>> situation. It might be interesting to see how much variation there is
>> between JVMs.
>>
>> Like others, I would only use regexp as a last resort in Java anyway;
>> compared to Perl, writing the code is painful. Still, I guess that you
>> know this!
>>
>> Phil
>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From to.petr at gmail.com  Wed Oct 24 14:10:38 2012
From: to.petr at gmail.com (P. Troshin)
Date: Wed, 24 Oct 2012 19:10:38 +0100
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <4F9982AE-FA76-41BF-BF1B-58B7889F03AB@drycafe.net>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<874nllo4fx.fsf@newcastle.ac.uk>
	<4F9982AE-FA76-41BF-BF1B-58B7889F03AB@drycafe.net>
Message-ID: <CAAT4F8mRXOVvRX9RyMBi1mzB_LPodYK2Z9Q+SiP6=W2q16uMLw@mail.gmail.com>

Hi Hilmar,

Hmm, it looks like I spoke too soon; the previous run was doing
nothing as all of the cases were commented out.
I can now see that the results of my runs are not massively different
from that of yours.
It would help if you could encourage your student to write a few unit
tests so that we know what you are trying to achieve and to simplify
the testing.

Just a thought

Thanks,
Peter



On 24 October 2012 17:47, Hilmar Lapp <hlapp at drycafe.net> wrote:
> Hi everyone,
>
> Thanks for all your responses. Indeed I know that the Java regex API isn't an enjoyable one to program with, and if the underlying task were about writing something from scratch, I'd be all for avoiding regex's too if the same thing could be achieved by string comparison.
>
> However, and of course I failed to say that initially, the task from which this query is originating is about converting a Perl script to Java (not because Perl is somehow bad, but because those Perl scripts have shown to be an obstacle to easy cross-platform installation of the - mostly Java - software they are a part of). That doesn't mean one couldn't in the course also rewrite the code that uses regular expressions to one that doesn't, but I also think it wise not to introduce multiple variables as a source of error at once.
>
> Some of the responses would be best answered by looking at the expressions and the code that uses them, so here are the two "benchmark" scripts.
>
> Java: https://gist.github.com/3940931
> Perl: https://gist.github.com/3940780
>
> I'm also copying Dongye Meng here, who is a CS student at UNC working with us on the project - if anyone has further wisdom to share about how to reduce the performance gap between the two versions, he'd surely appreciate.
>
>         -hilmar
>
> On Oct 23, 2012, at 6:42 AM, Phillip Lord wrote:
>
>> Hilmar Lapp <hlapp at drycafe.net> writes:
>>> They (at least as in java.util.regex) have been reported to me as
>>> performing much slower (by several orders of magnitude) than the regex
>>> implementation in Perl, and some simple benchmarking tests seem to
>>> bear that out. Even after scrutinizing the benchmark and finding
>>> nothing obvious, I'm still skeptical as to why this would be the case
>>> - naively I would have assumed that the underlying runtime library is
>>> implemented in C in both cases. But perhaps this is not true?
>>
>>
>> Well, the difference is that Perl is perl, while Java is not; it all
>> depends on the JVM, and libraries also. A quick shuftie at
>> the source for the open-jdk libraries suggests that the regexp searching
>> is done in Java -- it's not just a drop through to C. Always the problem
>> with performance optimisation on Java -- you are only optimising for one
>> situation. It might be interesting to see how much variation there is
>> between JVMs.
>>
>> Like others, I would only use regexp as a last resort in Java anyway;
>> compared to Perl, writing the code is painful. Still, I guess that you
>> know this!
>>
>> Phil
>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From to.petr at gmail.com  Wed Oct 24 14:30:16 2012
From: to.petr at gmail.com (P. Troshin)
Date: Wed, 24 Oct 2012 19:30:16 +0100
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <CAAT4F8mRXOVvRX9RyMBi1mzB_LPodYK2Z9Q+SiP6=W2q16uMLw@mail.gmail.com>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<874nllo4fx.fsf@newcastle.ac.uk>
	<4F9982AE-FA76-41BF-BF1B-58B7889F03AB@drycafe.net>
	<CAAT4F8mRXOVvRX9RyMBi1mzB_LPodYK2Z9Q+SiP6=W2q16uMLw@mail.gmail.com>
Message-ID: <CAAT4F8kT41E=p5OOn=EgPXdbFnQzOsMHej00Scpt1D2EN+tZ8Q@mail.gmail.com>

Hi Hilmar,

Looked at the test in a bit more details, I can see what you are
trying to test but is there a real life problem behind this?
What this test is doing is a lot of searches on very short strings. Is
this what your real life application does? I am asking because if your
real life application uses regexp to look into long string, the
performance might be totally different.
What is your aim - 3 seconds for 500K searches do not seem
particularly slow to me.

Thanks
Peter


On 24 October 2012 19:10, P. Troshin <to.petr at gmail.com> wrote:
> Hi Hilmar,
>
> Hmm, it looks like I spoke too soon; the previous run was doing
> nothing as all of the cases were commented out.
> I can now see that the results of my runs are not massively different
> from that of yours.
> It would help if you could encourage your student to write a few unit
> tests so that we know what you are trying to achieve and to simplify
> the testing.
>
> Just a thought
>
> Thanks,
> Peter
>
>
>
> On 24 October 2012 17:47, Hilmar Lapp <hlapp at drycafe.net> wrote:
>> Hi everyone,
>>
>> Thanks for all your responses. Indeed I know that the Java regex API isn't an enjoyable one to program with, and if the underlying task were about writing something from scratch, I'd be all for avoiding regex's too if the same thing could be achieved by string comparison.
>>
>> However, and of course I failed to say that initially, the task from which this query is originating is about converting a Perl script to Java (not because Perl is somehow bad, but because those Perl scripts have shown to be an obstacle to easy cross-platform installation of the - mostly Java - software they are a part of). That doesn't mean one couldn't in the course also rewrite the code that uses regular expressions to one that doesn't, but I also think it wise not to introduce multiple variables as a source of error at once.
>>
>> Some of the responses would be best answered by looking at the expressions and the code that uses them, so here are the two "benchmark" scripts.
>>
>> Java: https://gist.github.com/3940931
>> Perl: https://gist.github.com/3940780
>>
>> I'm also copying Dongye Meng here, who is a CS student at UNC working with us on the project - if anyone has further wisdom to share about how to reduce the performance gap between the two versions, he'd surely appreciate.
>>
>>         -hilmar
>>
>> On Oct 23, 2012, at 6:42 AM, Phillip Lord wrote:
>>
>>> Hilmar Lapp <hlapp at drycafe.net> writes:
>>>> They (at least as in java.util.regex) have been reported to me as
>>>> performing much slower (by several orders of magnitude) than the regex
>>>> implementation in Perl, and some simple benchmarking tests seem to
>>>> bear that out. Even after scrutinizing the benchmark and finding
>>>> nothing obvious, I'm still skeptical as to why this would be the case
>>>> - naively I would have assumed that the underlying runtime library is
>>>> implemented in C in both cases. But perhaps this is not true?
>>>
>>>
>>> Well, the difference is that Perl is perl, while Java is not; it all
>>> depends on the JVM, and libraries also. A quick shuftie at
>>> the source for the open-jdk libraries suggests that the regexp searching
>>> is done in Java -- it's not just a drop through to C. Always the problem
>>> with performance optimisation on Java -- you are only optimising for one
>>> situation. It might be interesting to see how much variation there is
>>> between JVMs.
>>>
>>> Like others, I would only use regexp as a last resort in Java anyway;
>>> compared to Perl, writing the code is painful. Still, I guess that you
>>> know this!
>>>
>>> Phil
>>
>> --
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>> ===========================================================
>>
>>
>>
>>
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l


From hlapp at drycafe.net  Wed Oct 24 23:45:52 2012
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 24 Oct 2012 23:45:52 -0400
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <CAAT4F8kT41E=p5OOn=EgPXdbFnQzOsMHej00Scpt1D2EN+tZ8Q@mail.gmail.com>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<874nllo4fx.fsf@newcastle.ac.uk>
	<4F9982AE-FA76-41BF-BF1B-58B7889F03AB@drycafe.net>
	<CAAT4F8mRXOVvRX9RyMBi1mzB_LPodYK2Z9Q+SiP6=W2q16uMLw@mail.gmail.com>
	<CAAT4F8kT41E=p5OOn=EgPXdbFnQzOsMHej00Scpt1D2EN+tZ8Q@mail.gmail.com>
Message-ID: <34DFDF13-5014-4383-A3D3-BAF793AC2E23@drycafe.net>

The code is a very small snippet from a natural language processing software aimed at extracting structured phenotype descriptions from un- or semistructured free text. Apparently the code as is (in Perl) makes a lot of regular expression matches, and so if the speed difference for them between Perl and Java is significant, in theory this might become a problem. Though whether it will or will not amount to a bottleneck indeed remains to be seen, as the code is also doing other things that are potentially expensive, and possibly more so than the regex matching. 

So the exercise here is merely to see whether there is a notable performance difference in regex pattern evaluation that can't simply be attributed to programming mistakes (and apparently there is).

	-hilmar

On Oct 24, 2012, at 2:30 PM, P. Troshin wrote:

> Hi Hilmar,
> 
> Looked at the test in a bit more details, I can see what you are
> trying to test but is there a real life problem behind this?
> What this test is doing is a lot of searches on very short strings. Is
> this what your real life application does? I am asking because if your
> real life application uses regexp to look into long string, the
> performance might be totally different.
> What is your aim - 3 seconds for 500K searches do not seem
> particularly slow to me.
> 
> Thanks
> Peter
> 
> 
> On 24 October 2012 19:10, P. Troshin <to.petr at gmail.com> wrote:
>> Hi Hilmar,
>> 
>> Hmm, it looks like I spoke too soon; the previous run was doing
>> nothing as all of the cases were commented out.
>> I can now see that the results of my runs are not massively different
>> from that of yours.
>> It would help if you could encourage your student to write a few unit
>> tests so that we know what you are trying to achieve and to simplify
>> the testing.
>> 
>> Just a thought
>> 
>> Thanks,
>> Peter
>> 
>> 
>> 
>> On 24 October 2012 17:47, Hilmar Lapp <hlapp at drycafe.net> wrote:
>>> Hi everyone,
>>> 
>>> Thanks for all your responses. Indeed I know that the Java regex API isn't an enjoyable one to program with, and if the underlying task were about writing something from scratch, I'd be all for avoiding regex's too if the same thing could be achieved by string comparison.
>>> 
>>> However, and of course I failed to say that initially, the task from which this query is originating is about converting a Perl script to Java (not because Perl is somehow bad, but because those Perl scripts have shown to be an obstacle to easy cross-platform installation of the - mostly Java - software they are a part of). That doesn't mean one couldn't in the course also rewrite the code that uses regular expressions to one that doesn't, but I also think it wise not to introduce multiple variables as a source of error at once.
>>> 
>>> Some of the responses would be best answered by looking at the expressions and the code that uses them, so here are the two "benchmark" scripts.
>>> 
>>> Java: https://gist.github.com/3940931
>>> Perl: https://gist.github.com/3940780
>>> 
>>> I'm also copying Dongye Meng here, who is a CS student at UNC working with us on the project - if anyone has further wisdom to share about how to reduce the performance gap between the two versions, he'd surely appreciate.
>>> 
>>>        -hilmar
>>> 
>>> On Oct 23, 2012, at 6:42 AM, Phillip Lord wrote:
>>> 
>>>> Hilmar Lapp <hlapp at drycafe.net> writes:
>>>>> They (at least as in java.util.regex) have been reported to me as
>>>>> performing much slower (by several orders of magnitude) than the regex
>>>>> implementation in Perl, and some simple benchmarking tests seem to
>>>>> bear that out. Even after scrutinizing the benchmark and finding
>>>>> nothing obvious, I'm still skeptical as to why this would be the case
>>>>> - naively I would have assumed that the underlying runtime library is
>>>>> implemented in C in both cases. But perhaps this is not true?
>>>> 
>>>> 
>>>> Well, the difference is that Perl is perl, while Java is not; it all
>>>> depends on the JVM, and libraries also. A quick shuftie at
>>>> the source for the open-jdk libraries suggests that the regexp searching
>>>> is done in Java -- it's not just a drop through to C. Always the problem
>>>> with performance optimisation on Java -- you are only optimising for one
>>>> situation. It might be interesting to see how much variation there is
>>>> between JVMs.
>>>> 
>>>> Like others, I would only use regexp as a last resort in Java anyway;
>>>> compared to Perl, writing the code is painful. Still, I guess that you
>>>> know this!
>>>> 
>>>> Phil
>>> 
>>> --
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> ===========================================================
>>> 
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From daniel.quest at gmail.com  Wed Oct 24 23:51:53 2012
From: daniel.quest at gmail.com (daniel.quest at gmail.com)
Date: Wed, 24 Oct 2012 22:51:53 -0500
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <34DFDF13-5014-4383-A3D3-BAF793AC2E23@drycafe.net>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<874nllo4fx.fsf@newcastle.ac.uk>
	<4F9982AE-FA76-41BF-BF1B-58B7889F03AB@drycafe.net>
	<CAAT4F8mRXOVvRX9RyMBi1mzB_LPodYK2Z9Q+SiP6=W2q16uMLw@mail.gmail.com>
	<CAAT4F8kT41E=p5OOn=EgPXdbFnQzOsMHej00Scpt1D2EN+tZ8Q@mail.gmail.com>
	<34DFDF13-5014-4383-A3D3-BAF793AC2E23@drycafe.net>
Message-ID: <AC1E9496-7603-4F55-A8BB-818DD1CD7786@gmail.com>

Have you ever used uima?  Same software used on the IBM Watson project.  Very very powerful.

http://uima.apache.org/

Dan

Sent from my iPhone

On Oct 24, 2012, at 10:45 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> The code is a very small snippet from a natural language processing software aimed at extracting structured phenotype descriptions from un- or semistructured free text. Apparently the code as is (in Perl) makes a lot of regular expression matches, and so if the speed difference for them between Perl and Java is significant, in theory this might become a problem. Though whether it will or will not amount to a bottleneck indeed remains to be seen, as the code is also doing other things that are potentially expensive, and possibly more so than the regex matching. 
> 
> So the exercise here is merely to see whether there is a notable performance difference in regex pattern evaluation that can't simply be attributed to programming mistakes (and apparently there is).
> 
>    -hilmar
> 
> On Oct 24, 2012, at 2:30 PM, P. Troshin wrote:
> 
>> Hi Hilmar,
>> 
>> Looked at the test in a bit more details, I can see what you are
>> trying to test but is there a real life problem behind this?
>> What this test is doing is a lot of searches on very short strings. Is
>> this what your real life application does? I am asking because if your
>> real life application uses regexp to look into long string, the
>> performance might be totally different.
>> What is your aim - 3 seconds for 500K searches do not seem
>> particularly slow to me.
>> 
>> Thanks
>> Peter
>> 
>> 
>> On 24 October 2012 19:10, P. Troshin <to.petr at gmail.com> wrote:
>>> Hi Hilmar,
>>> 
>>> Hmm, it looks like I spoke too soon; the previous run was doing
>>> nothing as all of the cases were commented out.
>>> I can now see that the results of my runs are not massively different
>>> from that of yours.
>>> It would help if you could encourage your student to write a few unit
>>> tests so that we know what you are trying to achieve and to simplify
>>> the testing.
>>> 
>>> Just a thought
>>> 
>>> Thanks,
>>> Peter
>>> 
>>> 
>>> 
>>> On 24 October 2012 17:47, Hilmar Lapp <hlapp at drycafe.net> wrote:
>>>> Hi everyone,
>>>> 
>>>> Thanks for all your responses. Indeed I know that the Java regex API isn't an enjoyable one to program with, and if the underlying task were about writing something from scratch, I'd be all for avoiding regex's too if the same thing could be achieved by string comparison.
>>>> 
>>>> However, and of course I failed to say that initially, the task from which this query is originating is about converting a Perl script to Java (not because Perl is somehow bad, but because those Perl scripts have shown to be an obstacle to easy cross-platform installation of the - mostly Java - software they are a part of). That doesn't mean one couldn't in the course also rewrite the code that uses regular expressions to one that doesn't, but I also think it wise not to introduce multiple variables as a source of error at once.
>>>> 
>>>> Some of the responses would be best answered by looking at the expressions and the code that uses them, so here are the two "benchmark" scripts.
>>>> 
>>>> Java: https://gist.github.com/3940931
>>>> Perl: https://gist.github.com/3940780
>>>> 
>>>> I'm also copying Dongye Meng here, who is a CS student at UNC working with us on the project - if anyone has further wisdom to share about how to reduce the performance gap between the two versions, he'd surely appreciate.
>>>> 
>>>>       -hilmar
>>>> 
>>>> On Oct 23, 2012, at 6:42 AM, Phillip Lord wrote:
>>>> 
>>>>> Hilmar Lapp <hlapp at drycafe.net> writes:
>>>>>> They (at least as in java.util.regex) have been reported to me as
>>>>>> performing much slower (by several orders of magnitude) than the regex
>>>>>> implementation in Perl, and some simple benchmarking tests seem to
>>>>>> bear that out. Even after scrutinizing the benchmark and finding
>>>>>> nothing obvious, I'm still skeptical as to why this would be the case
>>>>>> - naively I would have assumed that the underlying runtime library is
>>>>>> implemented in C in both cases. But perhaps this is not true?
>>>>> 
>>>>> 
>>>>> Well, the difference is that Perl is perl, while Java is not; it all
>>>>> depends on the JVM, and libraries also. A quick shuftie at
>>>>> the source for the open-jdk libraries suggests that the regexp searching
>>>>> is done in Java -- it's not just a drop through to C. Always the problem
>>>>> with performance optimisation on Java -- you are only optimising for one
>>>>> situation. It might be interesting to see how much variation there is
>>>>> between JVMs.
>>>>> 
>>>>> Like others, I would only use regexp as a last resort in Java anyway;
>>>>> compared to Perl, writing the code is painful. Still, I guess that you
>>>>> know this!
>>>>> 
>>>>> Phil
>>>> 
>>>> --
>>>> ===========================================================
>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>>> ===========================================================
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From andreas at sdsc.edu  Wed Oct 31 16:48:07 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 31 Oct 2012 13:48:07 -0700
Subject: [Biojava-l] open-bio servers moving
Message-ID: <CALthepw=Suuw8XU+xJJ==X5tZ-V_fAiritxeW-zkxra22y2Hqg@mail.gmail.com>

Hi,

The portal.open-bio.org server that is hosting the biojava wiki site is
currently down, since it is being moved to a new location on the Amazon
Cloud.

It may take a few days until everything has been set up properly and the
wiki will be back.

If there is anybody on the biojava side who wants to join the open
bioinformatics foundation's sysadmin team and help out with projects like
this one, this would be a good moment to volunteer...

Andreas

From daniel.quest at gmail.com  Wed Oct  3 03:31:46 2012
From: daniel.quest at gmail.com (Daniel Quest)
Date: Tue, 2 Oct 2012 22:31:46 -0500
Subject: [Biojava-l] maven + genbank parser
Message-ID: <CAHm=Cq7AHaR4bRjccVVY1diWBL6jbV227Qh+QRN4BB_rHF1GDw@mail.gmail.com>

Is there an example project that uses maven to access the genbank parser?
 I am confused if biojava3 has genbank support.  If I want to use an
earlier version along the lines of the cookbook does it exist in a maven
repo?

Thanks
Dan


From andreas at sdsc.edu  Wed Oct  3 05:09:28 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 2 Oct 2012 22:09:28 -0700
Subject: [Biojava-l] maven + genbank parser
In-Reply-To: <CAHm=Cq7AHaR4bRjccVVY1diWBL6jbV227Qh+QRN4BB_rHF1GDw@mail.gmail.com>
References: <CAHm=Cq7AHaR4bRjccVVY1diWBL6jbV227Qh+QRN4BB_rHF1GDw@mail.gmail.com>
Message-ID: <CALthepxwzDJeaViDyU8hjPNQWRQuWXhTpQ7KwH_MLVXn-Ra8bA@mail.gmail.com>

Hi Daniel,

both the 1.8 as well as the 3.0 series are available via maven builds.
You have to configure the biojava specific repo

<repositories>
		...
		<repository>
			<id>biojava-maven-repo</id>
			<name>BioJava repository</name>
			<url>http://www.biojava.org/download/maven/</url>			
		</repository>
	</repositories>

Andreas

On Tue, Oct 2, 2012 at 8:31 PM, Daniel Quest <daniel.quest at gmail.com> wrote:
> Is there an example project that uses maven to access the genbank parser?
>  I am confused if biojava3 has genbank support.  If I want to use an
> earlier version along the lines of the cookbook does it exist in a maven
> repo?
>
> Thanks
> Dan
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From andreas at sdsc.edu  Mon Oct  8 22:43:43 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 8 Oct 2012 15:43:43 -0700
Subject: [Biojava-l] InstabilityIndex
In-Reply-To: <1349723178.65392.YahooMailNeo@web190604.mail.sg3.yahoo.com>
References: <1349723178.65392.YahooMailNeo@web190604.mail.sg3.yahoo.com>
Message-ID: <CALthepyv+wTAk563YjqoUuY_umw-PHqfFU45GWSPGNwwywTE0g@mail.gmail.com>

Hi Subrata,

Please don't mail me directly, but send your questions to the list.
Chances are that somebody there can help you best.

Ah Fu, do you have any thoughts on this?

Thanks,

Andreas




On Mon, Oct 8, 2012 at 12:06 PM, subrata sinha
<subratasinha2006 at yahoo.co.in> wrote:
> Dear Sir,
>
> I was testing the getInstabilityIndex() method of
> org.biojava3.aaproperties.PeptideProperties class.
>
> I am trying to find InstabilityIndex for very short segment of peptide, as
> short as two. But I am getting some surprising result in negative.Then i
> found that the method perhaps giving -ve result for ambiguous characters. So
> how to handle a situation if my protein sequence contains ambiguous
> characters
>
> Input Sequence            Instability Index
>
> GTDG                      -13.725
> VDVR                      -30.075
>
> How i analyse the above situation.
>
> Kindly help me.
>
>
> With Regards
>
> Subrata Sinha
> Assistant Professor
> Centre for Bioinformatics Studies
> Dibrugarh University


From darnells at dnastar.com  Tue Oct  9 17:32:36 2012
From: darnells at dnastar.com (Steve Darnell)
Date: Tue, 9 Oct 2012 17:32:36 +0000
Subject: [Biojava-l] InstabilityIndex
In-Reply-To: <CALthepyv+wTAk563YjqoUuY_umw-PHqfFU45GWSPGNwwywTE0g@mail.gmail.com>
References: <1349723178.65392.YahooMailNeo@web190604.mail.sg3.yahoo.com>
	<CALthepyv+wTAk563YjqoUuY_umw-PHqfFU45GWSPGNwwywTE0g@mail.gmail.com>
Message-ID: <DFF89F3308438B4291689BA4BDD65D055961034C@MS1.dnastar.com>

@Subrata, The class does not handle characters other than the standard 20 amino acids. We substitute BJOUXZ with DLKCAE and live with the approximation.

@Ah Fu, In the past we have used average values for B (D or N), J (L or I), and Z (E or Q), and a dummy substitution for X (G or A). Our U and O substitutions just map to the closest natural amino acid. It would be nice if real values existed for selenocysteine and pyrrolysine, but I haven't a clue if they do.

@Andreas, I would suggest that a general policy that all protein sequence analyses support the 6 non-standard letter would be a good thing. A nice ideal, but who has the time? :)

Regards,
Steve

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic
Sent: Monday, October 08, 2012 5:44 PM
To: subrata sinha
Cc: Chuan Hock Koh; biojava-l at biojava.org
Subject: Re: [Biojava-l] InstabilityIndex

Hi Subrata,

Please don't mail me directly, but send your questions to the list.
Chances are that somebody there can help you best.

Ah Fu, do you have any thoughts on this?

Thanks,

Andreas




On Mon, Oct 8, 2012 at 12:06 PM, subrata sinha <subratasinha2006 at yahoo.co.in> wrote:
> Dear Sir,
>
> I was testing the getInstabilityIndex() method of 
> org.biojava3.aaproperties.PeptideProperties class.
>
> I am trying to find InstabilityIndex for very short segment of 
> peptide, as short as two. But I am getting some surprising result in 
> negative.Then i found that the method perhaps giving -ve result for 
> ambiguous characters. So how to handle a situation if my protein 
> sequence contains ambiguous characters
>
> Input Sequence            Instability Index
>
> GTDG                      -13.725
> VDVR                      -30.075
>
> How i analyse the above situation.
>
> Kindly help me.
>
>
> With Regards
>
> Subrata Sinha
> Assistant Professor
> Centre for Bioinformatics Studies
> Dibrugarh University
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l



From hlapp at drycafe.net  Wed Oct 10 20:31:04 2012
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 10 Oct 2012 16:31:04 -0400
Subject: [Biojava-l] Fwd: [Announce] Call for Proposals for Doc Sprint
	Summit v2.0
References: <CAEkQO62TQA7sge4ChRwO6HR6j42pvt-KfAcj_mEt3VfMmwsEOQ@mail.gmail.com>
Message-ID: <CA82E0D3-9336-4A93-8324-2EE80B0ECA9D@drycafe.net>

If you've been a Google Summer of Code mentor this year or last year, you will have already seen this. I wanted to make sure everybody is aware, and this may provide the opportunity for the kind of concerted effort that could finally get a BioPerl, Biopython, Bioruby, or Biojava (or a combined??) off the ground.

	-hilmar

Begin forwarded message:

From: Carol Smith <carols at google.com>
Subject: [GSoC Mentors] [Announce] Call for Proposals for Doc Sprint Summit v2.0
Date: October 10, 2012 2:44:50 PM EDT
To: Google Summer of Code Mentors List <google-summer-of-code-mentors-list at googlegroups.com>
Cc: adam at flossmanuals.net

Dear GSoC mentors and org admins, 

Google Summer of Code in collaboration with Aspiration and FLOSS Manuals is hosting a "Doc Sprint Camp" at Google's Mountain View headquarters (California) Dec 3 - 7, 2012.

The 2012 Doc Camp will feature:

1) An unconference on free software documentation topics - facilitated by Aspiration

2) 2-5 Book Sprints to produce books on free softwares - facilitated by FLOSS Manuals

Building on the success of the 2011 GSoC Doc Camp we are proud to bring you the 2012 GSoC Doc Camp. Like the previous event the 2012 GSoC Doc Camp is a place for free software communities to meet, create a book for their project, attract new people to their efforts, and share their documentation experiences. The camp aims to improve free documentation materials and skills in free software projects and individuals and help form the identity of the emergent free documentation sector.

Individuals and projects can apply. Food and accommodation for all individuals will be provided and travel support (full or partial) can also be applied for.

Be a part of this exciting event ? propose a Book Sprint on your favorite free software or come and help others write a book on their favorite project. Guaranteed to be a lot of fun, productive, and a fantastic place to advance your documentation efforts and experiences.

For more information or to register to take part, please see https://sites.google.com/site/docsprintsummitv2/. 

Please note proposals are due by October 26, so get yours in ASAP!

Cheers,
Carol Smith, Allen Gunn, Adam Hyde

-- 
You received this message because you are subscribed to the Google Groups "Google Summer of Code Mentors List" group.
To post to this group, send email to google-summer-of-code-mentors-list at googlegroups.com.
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-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================





-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================







From andreas at sdsc.edu  Thu Oct 11 02:17:45 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 10 Oct 2012 19:17:45 -0700
Subject: [Biojava-l] InstabilityIndex
In-Reply-To: <DFF89F3308438B4291689BA4BDD65D055961034C@MS1.dnastar.com>
References: <1349723178.65392.YahooMailNeo@web190604.mail.sg3.yahoo.com>
	<CALthepyv+wTAk563YjqoUuY_umw-PHqfFU45GWSPGNwwywTE0g@mail.gmail.com>
	<DFF89F3308438B4291689BA4BDD65D055961034C@MS1.dnastar.com>
Message-ID: <CALthepxHjaKZQL3CDMZkVddy=MbGDo0yshqLvVxDAidLpwHY+g@mail.gmail.com>

Thanks, good comments, Steve.

I agree we should make it a policy from now on to support 6
non-standard letters for anything protein related... About your time
comment - that's part of the idea of moving the development to git..
Ideally,  it should be easier for everybody who is concerned to patch
and share patches...

Andreas


On Tue, Oct 9, 2012 at 10:32 AM, Steve Darnell <darnells at dnastar.com> wrote:
> @Subrata, The class does not handle characters other than the standard 20 amino acids. We substitute BJOUXZ with DLKCAE and live with the approximation.
>
> @Ah Fu, In the past we have used average values for B (D or N), J (L or I), and Z (E or Q), and a dummy substitution for X (G or A). Our U and O substitutions just map to the closest natural amino acid. It would be nice if real values existed for selenocysteine and pyrrolysine, but I haven't a clue if they do.
>
> @Andreas, I would suggest that a general policy that all protein sequence analyses support the 6 non-standard letter would be a good thing. A nice ideal, but who has the time? :)
>
> Regards,
> Steve
>
> -----Original Message-----
> From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic
> Sent: Monday, October 08, 2012 5:44 PM
> To: subrata sinha
> Cc: Chuan Hock Koh; biojava-l at biojava.org
> Subject: Re: [Biojava-l] InstabilityIndex
>
> Hi Subrata,
>
> Please don't mail me directly, but send your questions to the list.
> Chances are that somebody there can help you best.
>
> Ah Fu, do you have any thoughts on this?
>
> Thanks,
>
> Andreas
>
>
>
>
> On Mon, Oct 8, 2012 at 12:06 PM, subrata sinha <subratasinha2006 at yahoo.co.in> wrote:
>> Dear Sir,
>>
>> I was testing the getInstabilityIndex() method of
>> org.biojava3.aaproperties.PeptideProperties class.
>>
>> I am trying to find InstabilityIndex for very short segment of
>> peptide, as short as two. But I am getting some surprising result in
>> negative.Then i found that the method perhaps giving -ve result for
>> ambiguous characters. So how to handle a situation if my protein
>> sequence contains ambiguous characters
>>
>> Input Sequence            Instability Index
>>
>> GTDG                      -13.725
>> VDVR                      -30.075
>>
>> How i analyse the above situation.
>>
>> Kindly help me.
>>
>>
>> With Regards
>>
>> Subrata Sinha
>> Assistant Professor
>> Centre for Bioinformatics Studies
>> Dibrugarh University
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l



From andreas.prlic at gmail.com  Thu Oct 11 18:32:30 2012
From: andreas.prlic at gmail.com (Andreas Prlic)
Date: Thu, 11 Oct 2012 11:32:30 -0700
Subject: [Biojava-l] Biojava Dependency on Forester
In-Reply-To: <CACHsrTvG_LCCZnh=uPdtE7H=5iAB3mZHXR_ZhwDYoyN5GqLgKw@mail.gmail.com>
References: <CACHsrTvG_LCCZnh=uPdtE7H=5iAB3mZHXR_ZhwDYoyN5GqLgKw@mail.gmail.com>
Message-ID: <CALthepzBRXUc2Yi+pnRpdtQ4T+AHXsQ3+0wdsEY_8_33rLZZfQ@mail.gmail.com>

Hi Terry,

Biojava depends on forester version 0.955. There are no plans to get
rid of this dependency, as far as I know. However we can try to
upgrade to a newer version if that helps.

If you are working in a Maven environment and you pull in BioJava that
way, you can add an exclusion to your config. Something like the XML
below. This forces your project to ignore the older forester library
configured in biojava. Is this a suitable workaround for your problem?

Andreas


	<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava3-phylo</artifactId>
			<version>3.0.4</version>
			<exclusions>
				<exclusion>
					<groupId>org</groupId>
					<artifactId>forester</artifactId>
				</exclusion>
			</exclusions>
		</dependency>




On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <tmc46 at cornell.edu> wrote:
> Dear Andreas,
>
> I am the lead developer of the software Tassel.
> http://www.maizegenetics.net/tassel
>
> We currently use Biojava 3.0.  And we are
> wanting to use the latest release of Forester.
> Since Biojava has a dependency on an older
> release of Forester, we are running into conflicts.
> Can you help explain Biojava's dependency on
> Forester?
>
> What version of Forester does Biojava 3.0 require?
> It looks like version 0.955
>
> What version of Forester does Biojava 3.0.4 require?
>
> Does any Biojava jar files include Forester classes?
> Or just references?
>
> Are there plans to remove Biojava's dependency
> on Forester?
>
>
> Thank you,
>
> Terry Casstevens


From andreas.prlic at gmail.com  Thu Oct 11 18:50:10 2012
From: andreas.prlic at gmail.com (Andreas Prlic)
Date: Thu, 11 Oct 2012 11:50:10 -0700
Subject: [Biojava-l] Biojava Dependency on Forester
In-Reply-To: <CACHsrTsteHwDm+wdOtLbHNxwqSRXpQ=JHRwTRRB_b0D4vx7VRQ@mail.gmail.com>
References: <CACHsrTvG_LCCZnh=uPdtE7H=5iAB3mZHXR_ZhwDYoyN5GqLgKw@mail.gmail.com>
	<CALthepzBRXUc2Yi+pnRpdtQ4T+AHXsQ3+0wdsEY_8_33rLZZfQ@mail.gmail.com>
	<CACHsrTsteHwDm+wdOtLbHNxwqSRXpQ=JHRwTRRB_b0D4vx7VRQ@mail.gmail.com>
Message-ID: <CALthepzyPJDJ-jsmn_in5c=1rPho6pTy+oWrBCkou4oBVH0a3Q@mail.gmail.com>

"exclusion" means only that the (old) forester.jar that biojava
depends on, will not be included. Instead you could configure your
newer forester dependency in its own <dependency> section. That one
will get used instead.

A

On Thu, Oct 11, 2012 at 11:43 AM, Terry Casstevens <tmc46 at cornell.edu> wrote:
> Hi Andreas,
>
> Thank you for the quick response!
>
> When you say "exclusion", sounds like the
> parts of biojava that uses forester would be excluded?
> I'm not sure, but I think our code uses some of
> the code that would be excluded.
>
> As you probably already know, the latest
> release of Forester is not backwardly
> compatible with Forester version 0.955.
>
> Thank you,
>
> Terry
>
>
> On Thu, Oct 11, 2012 at 2:32 PM, Andreas Prlic <andreas.prlic at gmail.com> wrote:
>> Hi Terry,
>>
>> Biojava depends on forester version 0.955. There are no plans to get
>> rid of this dependency, as far as I know. However we can try to
>> upgrade to a newer version if that helps.
>>
>> If you are working in a Maven environment and you pull in BioJava that
>> way, you can add an exclusion to your config. Something like the XML
>> below. This forces your project to ignore the older forester library
>> configured in biojava. Is this a suitable workaround for your problem?
>>
>> Andreas
>>
>>
>>         <dependency>
>>                         <groupId>org.biojava</groupId>
>>                         <artifactId>biojava3-phylo</artifactId>
>>                         <version>3.0.4</version>
>>                         <exclusions>
>>                                 <exclusion>
>>                                         <groupId>org</groupId>
>>                                         <artifactId>forester</artifactId>
>>                                 </exclusion>
>>                         </exclusions>
>>                 </dependency>
>>
>>
>>
>>
>> On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <tmc46 at cornell.edu> wrote:
>>> Dear Andreas,
>>>
>>> I am the lead developer of the software Tassel.
>>> http://www.maizegenetics.net/tassel
>>>
>>> We currently use Biojava 3.0.  And we are
>>> wanting to use the latest release of Forester.
>>> Since Biojava has a dependency on an older
>>> release of Forester, we are running into conflicts.
>>> Can you help explain Biojava's dependency on
>>> Forester?
>>>
>>> What version of Forester does Biojava 3.0 require?
>>> It looks like version 0.955
>>>
>>> What version of Forester does Biojava 3.0.4 require?
>>>
>>> Does any Biojava jar files include Forester classes?
>>> Or just references?
>>>
>>> Are there plans to remove Biojava's dependency
>>> on Forester?
>>>
>>>
>>> Thank you,
>>>
>>> Terry Casstevens


From HWillis at scripps.edu  Thu Oct 11 18:46:24 2012
From: HWillis at scripps.edu (Scooter Willis)
Date: Thu, 11 Oct 2012 14:46:24 -0400
Subject: [Biojava-l] Biojava Dependency on Forester
Message-ID: <9CA63734-A43D-4BAE-A744-FF292D1EF972@scripps.edu>

If forester has maven repository we can unhook the local depedency. We use forester for NJ and should only be a needed in one model. Let me know the issue/conflict and I can see what I can do to clean up.

Thanks

Scooter

----- Reply message -----
From: "Andreas Prlic" <andreas.prlic at gmail.com>
To: "Terry Casstevens" <tmc46 at cornell.edu>
Cc: "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz" <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>, "biojava-l at biojava.org" <biojava-l at biojava.org>
Subject: [Biojava-l] Biojava Dependency on Forester
Date: Thu, Oct 11, 2012 2:33 pm



Hi Terry,

Biojava depends on forester version 0.955. There are no plans to get
rid of this dependency, as far as I know. However we can try to
upgrade to a newer version if that helps.

If you are working in a Maven environment and you pull in BioJava that
way, you can add an exclusion to your config. Something like the XML
below. This forces your project to ignore the older forester library
configured in biojava. Is this a suitable workaround for your problem?

Andreas


        <dependency>
                        <groupId>org.biojava</groupId>
                        <artifactId>biojava3-phylo</artifactId>
                        <version>3.0.4</version>
                        <exclusions>
                                <exclusion>
                                        <groupId>org</groupId>
                                        <artifactId>forester</artifactId>
                                </exclusion>
                        </exclusions>
                </dependency>




On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <tmc46 at cornell.edu> wrote:
> Dear Andreas,
>
> I am the lead developer of the software Tassel.
> http://www.maizegenetics.net/tassel
>
> We currently use Biojava 3.0.  And we are
> wanting to use the latest release of Forester.
> Since Biojava has a dependency on an older
> release of Forester, we are running into conflicts.
> Can you help explain Biojava's dependency on
> Forester?
>
> What version of Forester does Biojava 3.0 require?
> It looks like version 0.955
>
> What version of Forester does Biojava 3.0.4 require?
>
> Does any Biojava jar files include Forester classes?
> Or just references?
>
> Are there plans to remove Biojava's dependency
> on Forester?
>
>
> Thank you,
>
> Terry Casstevens
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



From HWillis at scripps.edu  Thu Oct 11 19:50:26 2012
From: HWillis at scripps.edu (Scooter Willis)
Date: Thu, 11 Oct 2012 15:50:26 -0400
Subject: [Biojava-l] Biojava Dependency on Forester
Message-ID: <47E61FED-17CF-40E9-AE76-E44C11BDBB27@scripps.edu>

Andreas

Looks like the alignment code is using the distance matrix from forester and that has changed. Any chance the developer who did the MSA code could get this working with the latest forester code. It is probably a refactoring problem.

Scooter

----- Reply message -----
From: "Terry Casstevens" <tmc46 at cornell.edu>
To: "Scooter Willis" <HWillis at scripps.edu>
Cc: "Andreas Prlic" <andreas.prlic at gmail.com>, "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz" <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>, "biojava-l at biojava.org" <biojava-l at biojava.org>
Subject: [Biojava-l] Biojava Dependency on Forester
Date: Thu, Oct 11, 2012 2:56 pm



Hi Scooter, Andreas,

Thank you again for the responses.

This is one problem we are seeing.  org/forester/phylogenyinference
does not exist in Forester version 1.005.

Exception in thread "main" java.lang.NoClassDefFoundError:
org/forester/phylogenyinference/DistanceMatrix
at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176)
at net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java:306)
at net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java:183)
at net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.addSitesToMutableAlignment(TagsToSNPByAlignmentPlugin.java:417)
at net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.runTagsToSNPByAlignment(TagsToSNPByAlignmentPlugin.java:347)
at net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.performFunction(TagsToSNPByAlignmentPlugin.java:107)
at net.maizegenetics.gbs.pipeline.TerryPipelines.runTagsToSNPByAlignmentPlugin(TerryPipelines.java:36)
at net.maizegenetics.gbs.pipeline.TerryPipelines.main(TerryPipelines.java:41)
Caused by: java.lang.ClassNotFoundException:
org.forester.phylogenyinference.DistanceMatrix
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:356)


Thank you,

Terry


On Thu, Oct 11, 2012 at 2:46 PM, Scooter Willis <HWillis at scripps.edu> wrote:
> If forester has maven repository we can unhook the local depedency. We use
> forester for NJ and should only be a needed in one model. Let me know the
> issue/conflict and I can see what I can do to clean up.
>
> Thanks
>
> Scooter
>
>
> ----- Reply message -----
> From: "Andreas Prlic" <andreas.prlic at gmail.com>
> To: "Terry Casstevens" <tmc46 at cornell.edu>
> Cc: "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz"
> <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>,
> "biojava-l at biojava.org" <biojava-l at biojava.org>
> Subject: [Biojava-l] Biojava Dependency on Forester
> Date: Thu, Oct 11, 2012 2:33 pm
>
>
>
> Hi Terry,
>
> Biojava depends on forester version 0.955. There are no plans to get
> rid of this dependency, as far as I know. However we can try to
> upgrade to a newer version if that helps.
>
> If you are working in a Maven environment and you pull in BioJava that
> way, you can add an exclusion to your config. Something like the XML
> below. This forces your project to ignore the older forester library
> configured in biojava. Is this a suitable workaround for your problem?
>
> Andreas
>
>
>         <dependency>
>                         <groupId>org.biojava</groupId>
>                         <artifactId>biojava3-phylo</artifactId>
>                         <version>3.0.4</version>
>                         <exclusions>
>                                 <exclusion>
>                                         <groupId>org</groupId>
>                                         <artifactId>forester</artifactId>
>                                 </exclusion>
>                         </exclusions>
>                 </dependency>
>
>
>
>
> On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <tmc46 at cornell.edu>
> wrote:
>> Dear Andreas,
>>
>> I am the lead developer of the software Tassel.
>> http://www.maizegenetics.net/tassel
>>
>> We currently use Biojava 3.0.  And we are
>> wanting to use the latest release of Forester.
>> Since Biojava has a dependency on an older
>> release of Forester, we are running into conflicts.
>> Can you help explain Biojava's dependency on
>> Forester?
>>
>> What version of Forester does Biojava 3.0 require?
>> It looks like version 0.955
>>
>> What version of Forester does Biojava 3.0.4 require?
>>
>> Does any Biojava jar files include Forester classes?
>> Or just references?
>>
>> Are there plans to remove Biojava's dependency
>> on Forester?
>>
>>
>> Thank you,
>>
>> Terry Casstevens
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l



From kohchuanhock at gmail.com  Sun Oct 14 04:54:44 2012
From: kohchuanhock at gmail.com (Chuan Hock Koh)
Date: Sun, 14 Oct 2012 13:54:44 +0900
Subject: [Biojava-l] InstabilityIndex
In-Reply-To: <CALthepxHjaKZQL3CDMZkVddy=MbGDo0yshqLvVxDAidLpwHY+g@mail.gmail.com>
References: <1349723178.65392.YahooMailNeo@web190604.mail.sg3.yahoo.com>
	<CALthepyv+wTAk563YjqoUuY_umw-PHqfFU45GWSPGNwwywTE0g@mail.gmail.com>
	<DFF89F3308438B4291689BA4BDD65D055961034C@MS1.dnastar.com>
	<CALthepxHjaKZQL3CDMZkVddy=MbGDo0yshqLvVxDAidLpwHY+g@mail.gmail.com>
Message-ID: <CA+rQFrV5XQHCEPz8+T9JSj7mF3CioPqUByMOnKxsNOhjLtkhDQ@mail.gmail.com>

Hi Andreas and Steve,

Sorry for the slow response. Currently, I am in the midst of moving from
Singapore to Japan. Busy with settling into the new job, apartment hunting
etc..

So, what is the conclusion for the problem? Do let me know what you guys
like to be done, as clear as possible :)

I will code them whenever I can find time which I believe I should have
some at the end of this month.

Thanks,
Ah Fu


On Thu, Oct 11, 2012 at 11:17 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Thanks, good comments, Steve.
>
> I agree we should make it a policy from now on to support 6
> non-standard letters for anything protein related... About your time
> comment - that's part of the idea of moving the development to git..
> Ideally,  it should be easier for everybody who is concerned to patch
> and share patches...
>
> Andreas
>
>
> On Tue, Oct 9, 2012 at 10:32 AM, Steve Darnell <darnells at dnastar.com>
> wrote:
> > @Subrata, The class does not handle characters other than the standard
> 20 amino acids. We substitute BJOUXZ with DLKCAE and live with the
> approximation.
> >
> > @Ah Fu, In the past we have used average values for B (D or N), J (L or
> I), and Z (E or Q), and a dummy substitution for X (G or A). Our U and O
> substitutions just map to the closest natural amino acid. It would be nice
> if real values existed for selenocysteine and pyrrolysine, but I haven't a
> clue if they do.
> >
> > @Andreas, I would suggest that a general policy that all protein
> sequence analyses support the 6 non-standard letter would be a good thing.
> A nice ideal, but who has the time? :)
> >
> > Regards,
> > Steve
> >
> > -----Original Message-----
> > From: biojava-l-bounces at lists.open-bio.org [mailto:
> biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic
> > Sent: Monday, October 08, 2012 5:44 PM
> > To: subrata sinha
> > Cc: Chuan Hock Koh; biojava-l at biojava.org
> > Subject: Re: [Biojava-l] InstabilityIndex
> >
> > Hi Subrata,
> >
> > Please don't mail me directly, but send your questions to the list.
> > Chances are that somebody there can help you best.
> >
> > Ah Fu, do you have any thoughts on this?
> >
> > Thanks,
> >
> > Andreas
> >
> >
> >
> >
> > On Mon, Oct 8, 2012 at 12:06 PM, subrata sinha <
> subratasinha2006 at yahoo.co.in> wrote:
> >> Dear Sir,
> >>
> >> I was testing the getInstabilityIndex() method of
> >> org.biojava3.aaproperties.PeptideProperties class.
> >>
> >> I am trying to find InstabilityIndex for very short segment of
> >> peptide, as short as two. But I am getting some surprising result in
> >> negative.Then i found that the method perhaps giving -ve result for
> >> ambiguous characters. So how to handle a situation if my protein
> >> sequence contains ambiguous characters
> >>
> >> Input Sequence            Instability Index
> >>
> >> GTDG                      -13.725
> >> VDVR                      -30.075
> >>
> >> How i analyse the above situation.
> >>
> >> Kindly help me.
> >>
> >>
> >> With Regards
> >>
> >> Subrata Sinha
> >> Assistant Professor
> >> Centre for Bioinformatics Studies
> >> Dibrugarh University
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh<http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh/index.html>


From asidhu at biomap.org  Wed Oct 17 05:28:06 2012
From: asidhu at biomap.org (Amandeep Sidhu)
Date: Wed, 17 Oct 2012 13:28:06 +0800
Subject: [Biojava-l] International Symposium on Biomedical Data
	Infrastructure (BDI 2013)
Message-ID: <CAG_VK1TTWFYLunyqEWYhZEX08OUU9pQJno6e08ugmoxvhuK3KQ@mail.gmail.com>

International Symposium on Biomedical Data Infrastructure (BDI 2013)

30 - 31 January 2013

Kuala Lumpur, Malaysia

http://umconference.um.edu.my/BDI2013

Proceedings to be published by Springer

Due to the emerging demands of huge amounts of biomedical data, new and
improved data management capabilities are required for supporting a wide
range of applications. Current Biomedical Databases are independently
administered in geographically distinct locations, lending them almost
ideally to adoption of intelligent data management approaches. As a result
next generation of information infrastructure and data integration
capabilities are needed to ensure increasing infrastructure agility
required for high-throughput biomedical research. The workshop will focus
on research issues, problems and opportunities in Biomedical Data
Infrastructure.

Topics of Interest are:

* Big Biomedical Data and its Management
* Biomedical Data integration and Interoperability
* Next Generation Sequencing Data
* Biomedical Image Analysis
* Medical Informatics and Translational Bioinformatics
* Biomedical Ontologies
* Semantic Web Tools and Techniques for Biomedicine
* Web 2.0 and Web 3.0 Applications in Biomedicine
* Novel architectural models for HPC and cloud computing in Biomedicine
* New parallel / concurrent programming models for High Performance
Biomedical Applications in Cloud
* Biomedical Data Cloud
* Interoperability between different Utility Computing Platforms used for
Biomedicine
* Performance monitoring for biomedical applications in HPC and Cloud
* Biomedical Infrastructure as a Service
* Biomedical Platforms as a Service
* Biomedical Software as a Service
* Scientific workflows in bioinformatics and biomedicine
* Data Mining in Biomedicine
* Computational Systems Biology

Submission Guidelines:

We welcome original submissions that have not been published and that are
not under review by another conference or journal.  Papers should not
exceed 15 pages excluding references in Springer format. Paper should be
submitted through Easy Chair Online Submission System following
instructions on the website (http://umconference.um.edu.my/BDI2013). All
submissions will be evaluated on their originality, technical soundness,
significance, presentation, and interest to the symposium attendees.
Submission implies the willingness of at least one of the authors to
register and present the work associated with the paper submitted. All
submitted papers will be reviewed by symposium's technical program
committee. All accepted papers of registered authors will be included in
the proceedings published by Springer. All accepted papers will be required
to submit a Springer Copyright Form.

Important Dates:

Paper submission:               20 November 2012

Notifications sent to authors:  10 December 2012

Camera-ready papers due:        24 December 2012

Registration due:               10 January 2013

Conference:                     30 - 31 January 2013

Organizing Chairs:

Dr. Amandeep S. Sidhu (Curtin Sarawak Malaysia, Malaysia)
Dr. Sarinder Kaur (University of Malaya, Malaysia)

Steering Committee:

Dr. Dickson Lukose (MIMOS, Malaysia)
Dr. Kanagasabai Rajaraman (Institute for Infocomm Research, Singapore)
Prof. Dr. Meena Kishore Sakharkar (University of Tsukuba, Japan)
Prof. Dr. Jake Chen (Indiana University-Purdue University Indianapolis,
USA)
Prof. Dr. Xiaohua Tony Hu (Drexel University, USA)
Prof. Dr. Jason Tsong-Li Wang (New Jersey Institute of Technology, USA)
Prof. Dr. Carolyn McGregor (Health Informatics Research, Canada)

Please contact BDI 2013 Secretariat through email bdi at biomap.org for any
queries.


From chapman at cs.wisc.edu  Thu Oct 18 01:08:58 2012
From: chapman at cs.wisc.edu (Mark Chapman)
Date: Wed, 17 Oct 2012 20:08:58 -0500
Subject: [Biojava-l] Biojava Dependency on Forester
In-Reply-To: <47E61FED-17CF-40E9-AE76-E44C11BDBB27@scripps.edu>
References: <47E61FED-17CF-40E9-AE76-E44C11BDBB27@scripps.edu>
Message-ID: <507F56AA.3010001@cs.wisc.edu>

biojava3-alignment and biojava3-phylo have both been updated to use the 
latest forester release: 1.005.  The jar file is in our maven 
repository, and changes are committed to the SVN and git repositories.

Enjoy!
Mark


On 10/11/2012 02:50 PM, Scooter Willis wrote:
> Andreas
>
> Looks like the alignment code is using the distance matrix from forester and that has changed. Any chance the developer who did the MSA code could get this working with the latest forester code. It is probably a refactoring problem.
>
> Scooter
>
> ----- Reply message -----
> From: "Terry Casstevens" <tmc46 at cornell.edu>
> To: "Scooter Willis" <HWillis at scripps.edu>
> Cc: "Andreas Prlic" <andreas.prlic at gmail.com>, "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz" <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>, "biojava-l at biojava.org" <biojava-l at biojava.org>
> Subject: [Biojava-l] Biojava Dependency on Forester
> Date: Thu, Oct 11, 2012 2:56 pm
>
>
>
> Hi Scooter, Andreas,
>
> Thank you again for the responses.
>
> This is one problem we are seeing.  org/forester/phylogenyinference
> does not exist in Forester version 1.005.
>
> Exception in thread "main" java.lang.NoClassDefFoundError:
> org/forester/phylogenyinference/DistanceMatrix
> at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176)
> at net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java:306)
> at net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java:183)
> at net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.addSitesToMutableAlignment(TagsToSNPByAlignmentPlugin.java:417)
> at net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.runTagsToSNPByAlignment(TagsToSNPByAlignmentPlugin.java:347)
> at net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.performFunction(TagsToSNPByAlignmentPlugin.java:107)
> at net.maizegenetics.gbs.pipeline.TerryPipelines.runTagsToSNPByAlignmentPlugin(TerryPipelines.java:36)
> at net.maizegenetics.gbs.pipeline.TerryPipelines.main(TerryPipelines.java:41)
> Caused by: java.lang.ClassNotFoundException:
> org.forester.phylogenyinference.DistanceMatrix
> at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
> at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
>
>
> Thank you,
>
> Terry
>
>
> On Thu, Oct 11, 2012 at 2:46 PM, Scooter Willis <HWillis at scripps.edu> wrote:
>> If forester has maven repository we can unhook the local depedency. We use
>> forester for NJ and should only be a needed in one model. Let me know the
>> issue/conflict and I can see what I can do to clean up.
>>
>> Thanks
>>
>> Scooter
>>
>>
>> ----- Reply message -----
>> From: "Andreas Prlic" <andreas.prlic at gmail.com>
>> To: "Terry Casstevens" <tmc46 at cornell.edu>
>> Cc: "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz"
>> <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>,
>> "biojava-l at biojava.org" <biojava-l at biojava.org>
>> Subject: [Biojava-l] Biojava Dependency on Forester
>> Date: Thu, Oct 11, 2012 2:33 pm
>>
>>
>>
>> Hi Terry,
>>
>> Biojava depends on forester version 0.955. There are no plans to get
>> rid of this dependency, as far as I know. However we can try to
>> upgrade to a newer version if that helps.
>>
>> If you are working in a Maven environment and you pull in BioJava that
>> way, you can add an exclusion to your config. Something like the XML
>> below. This forces your project to ignore the older forester library
>> configured in biojava. Is this a suitable workaround for your problem?
>>
>> Andreas
>>
>>
>>          <dependency>
>>                          <groupId>org.biojava</groupId>
>>                          <artifactId>biojava3-phylo</artifactId>
>>                          <version>3.0.4</version>
>>                          <exclusions>
>>                                  <exclusion>
>>                                          <groupId>org</groupId>
>>                                          <artifactId>forester</artifactId>
>>                                  </exclusion>
>>                          </exclusions>
>>                  </dependency>
>>
>>
>>
>>
>> On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <tmc46 at cornell.edu>
>> wrote:
>>> Dear Andreas,
>>>
>>> I am the lead developer of the software Tassel.
>>> http://www.maizegenetics.net/tassel
>>>
>>> We currently use Biojava 3.0.  And we are
>>> wanting to use the latest release of Forester.
>>> Since Biojava has a dependency on an older
>>> release of Forester, we are running into conflicts.
>>> Can you help explain Biojava's dependency on
>>> Forester?
>>>
>>> What version of Forester does Biojava 3.0 require?
>>> It looks like version 0.955
>>>
>>> What version of Forester does Biojava 3.0.4 require?
>>>
>>> Does any Biojava jar files include Forester classes?
>>> Or just references?
>>>
>>> Are there plans to remove Biojava's dependency
>>> on Forester?
>>>
>>>
>>> Thank you,
>>>
>>> Terry Casstevens
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From andreas at sdsc.edu  Thu Oct 18 01:18:31 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 17 Oct 2012 18:18:31 -0700
Subject: [Biojava-l] Biojava Dependency on Forester
In-Reply-To: <507F56AA.3010001@cs.wisc.edu>
References: <47E61FED-17CF-40E9-AE76-E44C11BDBB27@scripps.edu>
	<507F56AA.3010001@cs.wisc.edu>
Message-ID: <CALthepycmnj9bOP04XyAOXthDS+jE=hJ1e5vd6xY-O91UbySPg@mail.gmail.com>

Awesome, Mark, Thanks for fixing this!

Andreas

On Wed, Oct 17, 2012 at 6:08 PM, Mark Chapman <chapman at cs.wisc.edu> wrote:
> biojava3-alignment and biojava3-phylo have both been updated to use the
> latest forester release: 1.005.  The jar file is in our maven repository,
> and changes are committed to the SVN and git repositories.
>
> Enjoy!
> Mark
>
>
>
> On 10/11/2012 02:50 PM, Scooter Willis wrote:
>>
>> Andreas
>>
>> Looks like the alignment code is using the distance matrix from forester
>> and that has changed. Any chance the developer who did the MSA code could
>> get this working with the latest forester code. It is probably a refactoring
>> problem.
>>
>> Scooter
>>
>> ----- Reply message -----
>> From: "Terry Casstevens" <tmc46 at cornell.edu>
>> To: "Scooter Willis" <HWillis at scripps.edu>
>> Cc: "Andreas Prlic" <andreas.prlic at gmail.com>, "Peter Bradbury"
>> <pjb39 at cornell.edu>, "Jeff Glaubitz" <jcg233 at cornell.edu>, "Ed Buckler"
>> <esb33 at cornell.edu>, "biojava-l at biojava.org" <biojava-l at biojava.org>
>> Subject: [Biojava-l] Biojava Dependency on Forester
>> Date: Thu, Oct 11, 2012 2:56 pm
>>
>>
>>
>> Hi Scooter, Andreas,
>>
>> Thank you again for the responses.
>>
>> This is one problem we are seeing.  org/forester/phylogenyinference
>> does not exist in Forester version 1.005.
>>
>> Exception in thread "main" java.lang.NoClassDefFoundError:
>> org/forester/phylogenyinference/DistanceMatrix
>> at
>> org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176)
>> at
>> net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java:306)
>> at
>> net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java:183)
>> at
>> net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.addSitesToMutableAlignment(TagsToSNPByAlignmentPlugin.java:417)
>> at
>> net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.runTagsToSNPByAlignment(TagsToSNPByAlignmentPlugin.java:347)
>> at
>> net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.performFunction(TagsToSNPByAlignmentPlugin.java:107)
>> at
>> net.maizegenetics.gbs.pipeline.TerryPipelines.runTagsToSNPByAlignmentPlugin(TerryPipelines.java:36)
>> at
>> net.maizegenetics.gbs.pipeline.TerryPipelines.main(TerryPipelines.java:41)
>> Caused by: java.lang.ClassNotFoundException:
>> org.forester.phylogenyinference.DistanceMatrix
>> at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
>> at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
>> at java.security.AccessController.doPrivileged(Native Method)
>> at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
>>
>>
>> Thank you,
>>
>> Terry
>>
>>
>> On Thu, Oct 11, 2012 at 2:46 PM, Scooter Willis <HWillis at scripps.edu>
>> wrote:
>>>
>>> If forester has maven repository we can unhook the local depedency. We
>>> use
>>> forester for NJ and should only be a needed in one model. Let me know the
>>> issue/conflict and I can see what I can do to clean up.
>>>
>>> Thanks
>>>
>>> Scooter
>>>
>>>
>>> ----- Reply message -----
>>> From: "Andreas Prlic" <andreas.prlic at gmail.com>
>>> To: "Terry Casstevens" <tmc46 at cornell.edu>
>>> Cc: "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz"
>>> <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>,
>>> "biojava-l at biojava.org" <biojava-l at biojava.org>
>>> Subject: [Biojava-l] Biojava Dependency on Forester
>>> Date: Thu, Oct 11, 2012 2:33 pm
>>>
>>>
>>>
>>> Hi Terry,
>>>
>>> Biojava depends on forester version 0.955. There are no plans to get
>>> rid of this dependency, as far as I know. However we can try to
>>> upgrade to a newer version if that helps.
>>>
>>> If you are working in a Maven environment and you pull in BioJava that
>>> way, you can add an exclusion to your config. Something like the XML
>>> below. This forces your project to ignore the older forester library
>>> configured in biojava. Is this a suitable workaround for your problem?
>>>
>>> Andreas
>>>
>>>
>>>          <dependency>
>>>                          <groupId>org.biojava</groupId>
>>>                          <artifactId>biojava3-phylo</artifactId>
>>>                          <version>3.0.4</version>
>>>                          <exclusions>
>>>                                  <exclusion>
>>>                                          <groupId>org</groupId>
>>>
>>> <artifactId>forester</artifactId>
>>>                                  </exclusion>
>>>                          </exclusions>
>>>                  </dependency>
>>>
>>>
>>>
>>>
>>> On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <tmc46 at cornell.edu>
>>> wrote:
>>>>
>>>> Dear Andreas,
>>>>
>>>> I am the lead developer of the software Tassel.
>>>> http://www.maizegenetics.net/tassel
>>>>
>>>> We currently use Biojava 3.0.  And we are
>>>> wanting to use the latest release of Forester.
>>>> Since Biojava has a dependency on an older
>>>> release of Forester, we are running into conflicts.
>>>> Can you help explain Biojava's dependency on
>>>> Forester?
>>>>
>>>> What version of Forester does Biojava 3.0 require?
>>>> It looks like version 0.955
>>>>
>>>> What version of Forester does Biojava 3.0.4 require?
>>>>
>>>> Does any Biojava jar files include Forester classes?
>>>> Or just references?
>>>>
>>>> Are there plans to remove Biojava's dependency
>>>> on Forester?
>>>>
>>>>
>>>> Thank you,
>>>>
>>>> Terry Casstevens
>>>
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From HWillis at scripps.edu  Thu Oct 18 01:49:24 2012
From: HWillis at scripps.edu (Scooter Willis)
Date: Wed, 17 Oct 2012 21:49:24 -0400
Subject: [Biojava-l] Biojava Dependency on Forester
In-Reply-To: <CALthepycmnj9bOP04XyAOXthDS+jE=hJ1e5vd6xY-O91UbySPg@mail.gmail.com>
Message-ID: <CCA4D816.1AB7A%hwillis@scripps.edu>

Thanks Mark! Is Forester on maven to avoid external jar file dependency?

On 10/17/12 9:18 PM, "Andreas Prlic" <andreas at sdsc.edu> wrote:

>Awesome, Mark, Thanks for fixing this!
>
>Andreas
>
>On Wed, Oct 17, 2012 at 6:08 PM, Mark Chapman <chapman at cs.wisc.edu> wrote:
>> biojava3-alignment and biojava3-phylo have both been updated to use the
>> latest forester release: 1.005.  The jar file is in our maven
>>repository,
>> and changes are committed to the SVN and git repositories.
>>
>> Enjoy!
>> Mark
>>
>>
>>
>> On 10/11/2012 02:50 PM, Scooter Willis wrote:
>>>
>>> Andreas
>>>
>>> Looks like the alignment code is using the distance matrix from
>>>forester
>>> and that has changed. Any chance the developer who did the MSA code
>>>could
>>> get this working with the latest forester code. It is probably a
>>>refactoring
>>> problem.
>>>
>>> Scooter
>>>
>>> ----- Reply message -----
>>> From: "Terry Casstevens" <tmc46 at cornell.edu>
>>> To: "Scooter Willis" <HWillis at scripps.edu>
>>> Cc: "Andreas Prlic" <andreas.prlic at gmail.com>, "Peter Bradbury"
>>> <pjb39 at cornell.edu>, "Jeff Glaubitz" <jcg233 at cornell.edu>, "Ed Buckler"
>>> <esb33 at cornell.edu>, "biojava-l at biojava.org" <biojava-l at biojava.org>
>>> Subject: [Biojava-l] Biojava Dependency on Forester
>>> Date: Thu, Oct 11, 2012 2:56 pm
>>>
>>>
>>>
>>> Hi Scooter, Andreas,
>>>
>>> Thank you again for the responses.
>>>
>>> This is one problem we are seeing.  org/forester/phylogenyinference
>>> does not exist in Forester version 1.005.
>>>
>>> Exception in thread "main" java.lang.NoClassDefFoundError:
>>> org/forester/phylogenyinference/DistanceMatrix
>>> at
>>> 
>>>org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignment
>>>s.java:176)
>>> at
>>> 
>>>net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java
>>>:306)
>>> at
>>> 
>>>net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java
>>>:183)
>>> at
>>> 
>>>net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.addSitesToMuta
>>>bleAlignment(TagsToSNPByAlignmentPlugin.java:417)
>>> at
>>> 
>>>net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.runTagsToSNPBy
>>>Alignment(TagsToSNPByAlignmentPlugin.java:347)
>>> at
>>> 
>>>net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.performFunctio
>>>n(TagsToSNPByAlignmentPlugin.java:107)
>>> at
>>> 
>>>net.maizegenetics.gbs.pipeline.TerryPipelines.runTagsToSNPByAlignmentPlu
>>>gin(TerryPipelines.java:36)
>>> at
>>> 
>>>net.maizegenetics.gbs.pipeline.TerryPipelines.main(TerryPipelines.java:4
>>>1)
>>> Caused by: java.lang.ClassNotFoundException:
>>> org.forester.phylogenyinference.DistanceMatrix
>>> at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
>>> at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
>>> at java.security.AccessController.doPrivileged(Native Method)
>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
>>>
>>>
>>> Thank you,
>>>
>>> Terry
>>>
>>>
>>> On Thu, Oct 11, 2012 at 2:46 PM, Scooter Willis <HWillis at scripps.edu>
>>> wrote:
>>>>
>>>> If forester has maven repository we can unhook the local depedency. We
>>>> use
>>>> forester for NJ and should only be a needed in one model. Let me know
>>>>the
>>>> issue/conflict and I can see what I can do to clean up.
>>>>
>>>> Thanks
>>>>
>>>> Scooter
>>>>
>>>>
>>>> ----- Reply message -----
>>>> From: "Andreas Prlic" <andreas.prlic at gmail.com>
>>>> To: "Terry Casstevens" <tmc46 at cornell.edu>
>>>> Cc: "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz"
>>>> <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>,
>>>> "biojava-l at biojava.org" <biojava-l at biojava.org>
>>>> Subject: [Biojava-l] Biojava Dependency on Forester
>>>> Date: Thu, Oct 11, 2012 2:33 pm
>>>>
>>>>
>>>>
>>>> Hi Terry,
>>>>
>>>> Biojava depends on forester version 0.955. There are no plans to get
>>>> rid of this dependency, as far as I know. However we can try to
>>>> upgrade to a newer version if that helps.
>>>>
>>>> If you are working in a Maven environment and you pull in BioJava that
>>>> way, you can add an exclusion to your config. Something like the XML
>>>> below. This forces your project to ignore the older forester library
>>>> configured in biojava. Is this a suitable workaround for your problem?
>>>>
>>>> Andreas
>>>>
>>>>
>>>>          <dependency>
>>>>                          <groupId>org.biojava</groupId>
>>>>                          <artifactId>biojava3-phylo</artifactId>
>>>>                          <version>3.0.4</version>
>>>>                          <exclusions>
>>>>                                  <exclusion>
>>>>                                          <groupId>org</groupId>
>>>>
>>>> <artifactId>forester</artifactId>
>>>>                                  </exclusion>
>>>>                          </exclusions>
>>>>                  </dependency>
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <tmc46 at cornell.edu>
>>>> wrote:
>>>>>
>>>>> Dear Andreas,
>>>>>
>>>>> I am the lead developer of the software Tassel.
>>>>> http://www.maizegenetics.net/tassel
>>>>>
>>>>> We currently use Biojava 3.0.  And we are
>>>>> wanting to use the latest release of Forester.
>>>>> Since Biojava has a dependency on an older
>>>>> release of Forester, we are running into conflicts.
>>>>> Can you help explain Biojava's dependency on
>>>>> Forester?
>>>>>
>>>>> What version of Forester does Biojava 3.0 require?
>>>>> It looks like version 0.955
>>>>>
>>>>> What version of Forester does Biojava 3.0.4 require?
>>>>>
>>>>> Does any Biojava jar files include Forester classes?
>>>>> Or just references?
>>>>>
>>>>> Are there plans to remove Biojava's dependency
>>>>> on Forester?
>>>>>
>>>>>
>>>>> Thank you,
>>>>>
>>>>> Terry Casstevens
>>>>
>>>> _______________________________________________
>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>>
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/biojava-l




From pwrose at ucsd.edu  Thu Oct 18 23:24:43 2012
From: pwrose at ucsd.edu (Peter Rose)
Date: Thu, 18 Oct 2012 23:24:43 +0000
Subject: [Biojava-l] [Job] Lead Web Architect - RCSB PDB
Message-ID: <B5E8EA0C57E75444B91F041CD98E10E90BCA2810@XMAIL-MBX-AT1.AD.UCSD.EDU>

Become part of the RCSB Protein Data Bank team. We have an opening for an experienced Lead Web Architect.

A detailed job description and online application form can be found at:
http://jobs.ucsd.edu/bulletin/job.aspx?cat=information&sortby=post&jobnum_in=64091

Qualifications:

* MS Degree in Computer Science or comparable combination of education and experience with considerable focus in Java EE software development.

* Established demonstrated work experience in the role of an architect and developer on medium to large size database-driven web applications using Java EE technology and standards.

* Advanced experience developing the presentation layer of a dynamic, database-driven web application using HTML, CSS, JavaScript, JavaScript Toolkits, Ajax, JSP, XML, Java. Experience resolving browser and cross-platform compatibility issues. Advanced experience with Struts2, Tiles, jQuery.

* Advanced experience with database design, Structured Query Language and RDBMS's such as MySQL. Expertise in web application server administration and configuration such as Tomcat.

* Established expertise in software life cycle methodologies. Experience with build tools such as Maven and Ant, and continuous integration systems such as Cruise Control. Experience with project tracking tools such as Jira.

________________________________________________
Peter Rose, Ph.D.
Scientific Lead
RCSB Protein Data Bank (http://www.rcsb.org)

San Diego Supercomputer Center (SDSC) and
Skaggs School of Pharmacy and Pharmaceutical Sciences
University of California San Diego





From hlapp at drycafe.net  Mon Oct 22 14:52:24 2012
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Mon, 22 Oct 2012 10:52:24 -0400
Subject: [Biojava-l] regex performance in Java
Message-ID: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>

I know that this is really Java language topic, but since parsing biological data formats is to rife with regular expression applications, I'm curious what the experience is among the Biojava people with the use of regular expressions in Java. 

They (at least as in java.util.regex) have been reported to me as performing much slower (by several orders of magnitude) than the regex implementation in Perl, and some simple benchmarking tests seem to bear that out. Even after scrutinizing the benchmark and finding nothing obvious, I'm still skeptical as to why this would be the case - naively I would have assumed that the underlying runtime library is implemented in C in both cases. But perhaps this is not true?

Any experience people have made here speed-wise (or tricks or things not to do for Java regex's) would be appreciated.

	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================







From andreas at sdsc.edu  Mon Oct 22 20:42:00 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 22 Oct 2012 13:42:00 -0700
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
Message-ID: <CALthepz64964iGpQ55J43hVw_9Gsgx8AfVFsKsKwo4HRToYf_Q@mail.gmail.com>

Hi Hilmar,

I can't say much about performance of java regular expressions, but
isn't it hard to write efficient regular expressions in any language?
There are great tools in the Java world for parsing of XML/JSON and
other standard file types that help avoiding them. I am not sure if
this is a general rule for the wider Java community, but from my
perspective, the use of regular expressions in Java is only limited
and used if nothing else works... Not sure if anybody else has a
different experience?

Andreas



On Mon, Oct 22, 2012 at 7:52 AM, Hilmar Lapp <hlapp at drycafe.net> wrote:
> I know that this is really Java language topic, but since parsing biological data formats is to rife with regular expression applications, I'm curious what the experience is among the Biojava people with the use of regular expressions in Java.
>
> They (at least as in java.util.regex) have been reported to me as performing much slower (by several orders of magnitude) than the regex implementation in Perl, and some simple benchmarking tests seem to bear that out. Even after scrutinizing the benchmark and finding nothing obvious, I'm still skeptical as to why this would be the case - naively I would have assumed that the underlying runtime library is implemented in C in both cases. But perhaps this is not true?
>
> Any experience people have made here speed-wise (or tricks or things not to do for Java regex's) would be appreciated.
>
>         -hilmar
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l



From to.petr at gmail.com  Mon Oct 22 20:48:02 2012
From: to.petr at gmail.com (P. Troshin)
Date: Mon, 22 Oct 2012 21:48:02 +0100
Subject: [Biojava-l] Fwd:  regex performance in Java
In-Reply-To: <CAAT4F8ndmJLuCuidA5Yt1mVwp1=gLgVgRuXSqd3J0T_sYu00ew@mail.gmail.com>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<CAAT4F8ndmJLuCuidA5Yt1mVwp1=gLgVgRuXSqd3J0T_sYu00ew@mail.gmail.com>
Message-ID: <CAAT4F8mdvuAwBSb1NAARJ_2rEVaK+rWWiQ8MtWZaYXGdgADYeA@mail.gmail.com>

Sorry, I should have written to the list. Also just want to say that I
agree with Andreas, in Java we use regexp if everything else fails
(:-))

Regards,
P.



---------- Forwarded message ----------
From: P. Troshin <to.petr at gmail.com>
Date: 22 October 2012 21:44
Subject: Re: [Biojava-l] regex performance in Java
To: Hilmar Lapp <hlapp at drycafe.net>


Hi Hilmar,

I think this is one of the myths, I do not think there is a
difference. It might have been true long ago, but I do not think this
is still the case. Last time we compared Perl, Python and Java
performance the former was the last with a large margin :-).  However,
I never had to make a direct comparison of regexp. Google for "perl vs
java regexp speed comparison" brings a few links. I had a quick look
at one result only
(http://onlyjob.blogspot.co.uk/2011/03/perl5-python-ruby-php-c-c-lua-tcl.html),
it claimed that Perl regexp is faster than Java. Unfortunately the
author of the test clearly lacked understanding of Java and as a
result the test compared the performance of String concatenation
(which is notoriously bad in Java, as Strings are immutable) rather
than the regexp performance itself. I guess this is an easy mistake to
make though. Hence the advice - if you are doing a lot of String
permutations use the StringBuilder class, not the String itself.
If you have a Java implementation which is lacking I am sure people on
this list will have no problem optimizing it!

Regards,
Peter



On 22 October 2012 15:52, Hilmar Lapp <hlapp at drycafe.net> wrote:
> I know that this is really Java language topic, but since parsing biological data formats is to rife with regular expression applications, I'm curious what the experience is among the Biojava people with the use of regular expressions in Java.
>
> They (at least as in java.util.regex) have been reported to me as performing much slower (by several orders of magnitude) than the regex implementation in Perl, and some simple benchmarking tests seem to bear that out. Even after scrutinizing the benchmark and finding nothing obvious, I'm still skeptical as to why this would be the case - naively I would have assumed that the underlying runtime library is implemented in C in both cases. But perhaps this is not true?
>
> Any experience people have made here speed-wise (or tricks or things not to do for Java regex's) would be appreciated.
>
>         -hilmar
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l



From tiagoantao at gmail.com  Mon Oct 22 20:53:56 2012
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Mon, 22 Oct 2012 21:53:56 +0100
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <CALthepz64964iGpQ55J43hVw_9Gsgx8AfVFsKsKwo4HRToYf_Q@mail.gmail.com>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<CALthepz64964iGpQ55J43hVw_9Gsgx8AfVFsKsKwo4HRToYf_Q@mail.gmail.com>
Message-ID: <CAA9RGEMmrX2-PQ-u878tj9Xs24VUBAaKZPxmTdiy=--747nJXg@mail.gmail.com>

On Mon, Oct 22, 2012 at 9:42 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> and used if nothing else works... Not sure if anybody else has a
> different experience?

I might be beating a dead horse here, but I agree. I would say that
from an idiomatic perspective Perl uses a lot of regex programming
(Ruby also?), which is less common in most other languages (Java and
Python are my work case). Regexes exist but are not the first option.
That being said, there is a very cool JVM language which has regexes
as first class objects: Clojure. But even in that case, I do not see
lots of idiomatic use of regexes.

Tiago


From daniel.quest at gmail.com  Tue Oct 23 04:51:37 2012
From: daniel.quest at gmail.com (daniel.quest at gmail.com)
Date: Mon, 22 Oct 2012 23:51:37 -0500
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <CAA9RGEMmrX2-PQ-u878tj9Xs24VUBAaKZPxmTdiy=--747nJXg@mail.gmail.com>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<CALthepz64964iGpQ55J43hVw_9Gsgx8AfVFsKsKwo4HRToYf_Q@mail.gmail.com>
	<CAA9RGEMmrX2-PQ-u878tj9Xs24VUBAaKZPxmTdiy=--747nJXg@mail.gmail.com>
Message-ID: <B9B6FF20-971C-4986-BA71-5475C44C6015@gmail.com>

Wow!  This could open a huge flame war.  Let me just make a couple of quick points about performance.

Perl is implemented in C/C++, It is interpreted, and Java runs bytecode on top of the JVM.  The Venders of JVMs probably write the bytecode instruction set in C/assembly.  Java itself, at least at this point is most likely written in Java.  The speed of Java is greatly influenced by the underlying JVM and how well the JVM instruction set maps to the hardware.  The algorithm being implemented and the version of Java also have a great impact on performance.  Conventional wisdom is that Fortran is the best performing language in widespread use with interpreted languages such as Python, Ruby, and Perl being 3-8 times slower.  This website shows Java having about a ten percent overhead relative to C:  http://shootout.alioth.debian.org/

I have personally noticed superior performance of Perl's Regex parsing capabilities over Python. I have never noticed a difference between Perl and Java that was so extreme that I would choose to implement something in Perl over Java in a production setting.  Java is a language with such deep library support that it makes most every language look like a second class citizen in comparison (notable exceptions: C, C++, and JavaScript)

Something else interesting: http://swtch.com/~rsc/regexp/regexp1.html

Finally, be very cautious of benchmarks.  It is very very hard to do benchmarking well.
Dan 
Sent from my iPhone

On Oct 22, 2012, at 3:53 PM, Tiago Ant?o <tiagoantao at gmail.com> wrote:

> On Mon, Oct 22, 2012 at 9:42 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> and used if nothing else works... Not sure if anybody else has a
>> different experience?
> 
> I might be beating a dead horse here, but I agree. I would say that
> from an idiomatic perspective Perl uses a lot of regex programming
> (Ruby also?), which is less common in most other languages (Java and
> Python are my work case). Regexes exist but are not the first option.
> That being said, there is a very cool JVM language which has regexes
> as first class objects: Clojure. But even in that case, I do not see
> lots of idiomatic use of regexes.
> 
> Tiago
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l



From khalil.elmazouari at gmail.com  Tue Oct 23 16:48:32 2012
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Tue, 23 Oct 2012 18:48:32 +0200
Subject: [Biojava-l] Biojava-l Digest, Vol 117, Issue 10
In-Reply-To: <mailman.1.1350921602.23329.biojava-l@lists.open-bio.org>
References: <mailman.1.1350921602.23329.biojava-l@lists.open-bio.org>
Message-ID: <99D2DB4A-DD8B-4473-BE04-2834ECF5457E@gmail.com>

Hi Hilmar,

I used regex a lot in perl and java... I was also skeptical about the regex in java when I start using them. 

from my own experience, I can tell you the following:
it's MUCH more easy to write regex in perl than in java.
java regex require more optimisation: working regex and optimal regex are two different things
in java, Patterns must be compiled first. So, if you iterate through a large number of strings you want to match, compile your pattern outside the loop
if you use regex in large iteration, avoid using methods from java.lang.String that use regex: String.replaceFirst, String.replaceAll, String.matches.... your pattern will be compiled each time
Avoid applying regex to large string. If possible, try to limit the matches to the places where the pattern is .. methods like indexOf, lastIndexOf, split ... from java.lang.String are very useful in this regards.
It's more easy to get the matching group in java than in perl
test first with editors like : RegExhibit or your IDE regex plugin.
finally, I recommend the Java Regular Expressions book from Mehran Habibi (http://www.amazon.com/Java-Regular-Expressions-Taming-java-util-regex/dp/1590591070)

If your regex are well optimised, you will not notice any difference between perl/java. 

If you need to use regex in complex algorithm or software in combination with java/biojava, don't hesitate, java regex are excellent. If you just need regex in small script go for perl

Best

khalil 



On 22 Oct 2012, at 18:00, biojava-l-request at lists.open-bio.org wrote:

> Send Biojava-l mailing list submissions to
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> 
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> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Biojava-l digest..."
> 
> 
> Today's Topics:
> 
>   1. regex performance in Java (Hilmar Lapp)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 22 Oct 2012 10:52:24 -0400
> From: Hilmar Lapp <hlapp at drycafe.net>
> Subject: [Biojava-l] regex performance in Java
> To: BioJava <biojava-l at biojava.org>
> Message-ID: <1B62BC3E-B005-4484-AE66-0B8F407E4756 at drycafe.net>
> Content-Type: text/plain; charset=us-ascii
> 
> I know that this is really Java language topic, but since parsing biological data formats is to rife with regular expression applications, I'm curious what the experience is among the Biojava people with the use of regular expressions in Java. 
> 
> They (at least as in java.util.regex) have been reported to me as performing much slower (by several orders of magnitude) than the regex implementation in Perl, and some simple benchmarking tests seem to bear that out. Even after scrutinizing the benchmark and finding nothing obvious, I'm still skeptical as to why this would be the case - naively I would have assumed that the underlying runtime library is implemented in C in both cases. But perhaps this is not true?
> 
> Any experience people have made here speed-wise (or tricks or things not to do for Java regex's) would be appreciated.
> 
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 
> End of Biojava-l Digest, Vol 117, Issue 10
> ******************************************





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From hlapp at drycafe.net  Wed Oct 24 16:47:27 2012
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 24 Oct 2012 12:47:27 -0400
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <874nllo4fx.fsf@newcastle.ac.uk>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<874nllo4fx.fsf@newcastle.ac.uk>
Message-ID: <4F9982AE-FA76-41BF-BF1B-58B7889F03AB@drycafe.net>

Hi everyone, 

Thanks for all your responses. Indeed I know that the Java regex API isn't an enjoyable one to program with, and if the underlying task were about writing something from scratch, I'd be all for avoiding regex's too if the same thing could be achieved by string comparison. 

However, and of course I failed to say that initially, the task from which this query is originating is about converting a Perl script to Java (not because Perl is somehow bad, but because those Perl scripts have shown to be an obstacle to easy cross-platform installation of the - mostly Java - software they are a part of). That doesn't mean one couldn't in the course also rewrite the code that uses regular expressions to one that doesn't, but I also think it wise not to introduce multiple variables as a source of error at once.

Some of the responses would be best answered by looking at the expressions and the code that uses them, so here are the two "benchmark" scripts.

Java: https://gist.github.com/3940931
Perl: https://gist.github.com/3940780

I'm also copying Dongye Meng here, who is a CS student at UNC working with us on the project - if anyone has further wisdom to share about how to reduce the performance gap between the two versions, he'd surely appreciate.

	-hilmar

On Oct 23, 2012, at 6:42 AM, Phillip Lord wrote:

> Hilmar Lapp <hlapp at drycafe.net> writes:
>> They (at least as in java.util.regex) have been reported to me as
>> performing much slower (by several orders of magnitude) than the regex
>> implementation in Perl, and some simple benchmarking tests seem to
>> bear that out. Even after scrutinizing the benchmark and finding
>> nothing obvious, I'm still skeptical as to why this would be the case
>> - naively I would have assumed that the underlying runtime library is
>> implemented in C in both cases. But perhaps this is not true?
> 
> 
> Well, the difference is that Perl is perl, while Java is not; it all
> depends on the JVM, and libraries also. A quick shuftie at
> the source for the open-jdk libraries suggests that the regexp searching
> is done in Java -- it's not just a drop through to C. Always the problem
> with performance optimisation on Java -- you are only optimising for one
> situation. It might be interesting to see how much variation there is
> between JVMs. 
> 
> Like others, I would only use regexp as a last resort in Java anyway;
> compared to Perl, writing the code is painful. Still, I guess that you
> know this!
> 
> Phil

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================







From to.petr at gmail.com  Wed Oct 24 17:59:19 2012
From: to.petr at gmail.com (P. Troshin)
Date: Wed, 24 Oct 2012 18:59:19 +0100
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <4F9982AE-FA76-41BF-BF1B-58B7889F03AB@drycafe.net>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<874nllo4fx.fsf@newcastle.ac.uk>
	<4F9982AE-FA76-41BF-BF1B-58B7889F03AB@drycafe.net>
Message-ID: <CAAT4F8=St=OseUtdgY_ZbU4-226cXoyQBKmxdeZW6u+h8sq84A@mail.gmail.com>

Hi Hilmar,

You have not mentions the version of JVM you are using, but it appears
that there is a massive difference in timing on my machine.
Here is the timing of the run on Windows 7 (pro 64 bit) with Oracle
JVM (64 bit) v. 1.7.0_02.

# of Iteration: 1t
Time: 1.711E-6 seconds

# of Iteration: 10
Time: 1.711E-6 seconds

# of Iteration: 100
Time: 2.567E-6 seconds

# of Iteration: 1000
Time: 1.2403E-5 seconds

# of Iteration: 10000
Time: 1.44143E-4 seconds

# of Iteration: 100000
Time: 0.001369138 seconds

I have not changed the code at all.
I have 3 year old laptop with Intel Core Duo P8600, 2.4 Ghz CPU. So
nothing special.
I cannot tell whether this is slow or not as you did not publish the
timings for Perl. Could you please do so.

It looks to me that you might just need to update/replace your JVM. I
will be happy to look at the code in a bit more details if this result
is still slower than Perl.

Thanks,
Peter



On 24 October 2012 17:47, Hilmar Lapp <hlapp at drycafe.net> wrote:
> Hi everyone,
>
> Thanks for all your responses. Indeed I know that the Java regex API isn't an enjoyable one to program with, and if the underlying task were about writing something from scratch, I'd be all for avoiding regex's too if the same thing could be achieved by string comparison.
>
> However, and of course I failed to say that initially, the task from which this query is originating is about converting a Perl script to Java (not because Perl is somehow bad, but because those Perl scripts have shown to be an obstacle to easy cross-platform installation of the - mostly Java - software they are a part of). That doesn't mean one couldn't in the course also rewrite the code that uses regular expressions to one that doesn't, but I also think it wise not to introduce multiple variables as a source of error at once.
>
> Some of the responses would be best answered by looking at the expressions and the code that uses them, so here are the two "benchmark" scripts.
>
> Java: https://gist.github.com/3940931
> Perl: https://gist.github.com/3940780
>
> I'm also copying Dongye Meng here, who is a CS student at UNC working with us on the project - if anyone has further wisdom to share about how to reduce the performance gap between the two versions, he'd surely appreciate.
>
>         -hilmar
>
> On Oct 23, 2012, at 6:42 AM, Phillip Lord wrote:
>
>> Hilmar Lapp <hlapp at drycafe.net> writes:
>>> They (at least as in java.util.regex) have been reported to me as
>>> performing much slower (by several orders of magnitude) than the regex
>>> implementation in Perl, and some simple benchmarking tests seem to
>>> bear that out. Even after scrutinizing the benchmark and finding
>>> nothing obvious, I'm still skeptical as to why this would be the case
>>> - naively I would have assumed that the underlying runtime library is
>>> implemented in C in both cases. But perhaps this is not true?
>>
>>
>> Well, the difference is that Perl is perl, while Java is not; it all
>> depends on the JVM, and libraries also. A quick shuftie at
>> the source for the open-jdk libraries suggests that the regexp searching
>> is done in Java -- it's not just a drop through to C. Always the problem
>> with performance optimisation on Java -- you are only optimising for one
>> situation. It might be interesting to see how much variation there is
>> between JVMs.
>>
>> Like others, I would only use regexp as a last resort in Java anyway;
>> compared to Perl, writing the code is painful. Still, I guess that you
>> know this!
>>
>> Phil
>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l



From to.petr at gmail.com  Wed Oct 24 18:10:38 2012
From: to.petr at gmail.com (P. Troshin)
Date: Wed, 24 Oct 2012 19:10:38 +0100
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <4F9982AE-FA76-41BF-BF1B-58B7889F03AB@drycafe.net>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<874nllo4fx.fsf@newcastle.ac.uk>
	<4F9982AE-FA76-41BF-BF1B-58B7889F03AB@drycafe.net>
Message-ID: <CAAT4F8mRXOVvRX9RyMBi1mzB_LPodYK2Z9Q+SiP6=W2q16uMLw@mail.gmail.com>

Hi Hilmar,

Hmm, it looks like I spoke too soon; the previous run was doing
nothing as all of the cases were commented out.
I can now see that the results of my runs are not massively different
from that of yours.
It would help if you could encourage your student to write a few unit
tests so that we know what you are trying to achieve and to simplify
the testing.

Just a thought

Thanks,
Peter



On 24 October 2012 17:47, Hilmar Lapp <hlapp at drycafe.net> wrote:
> Hi everyone,
>
> Thanks for all your responses. Indeed I know that the Java regex API isn't an enjoyable one to program with, and if the underlying task were about writing something from scratch, I'd be all for avoiding regex's too if the same thing could be achieved by string comparison.
>
> However, and of course I failed to say that initially, the task from which this query is originating is about converting a Perl script to Java (not because Perl is somehow bad, but because those Perl scripts have shown to be an obstacle to easy cross-platform installation of the - mostly Java - software they are a part of). That doesn't mean one couldn't in the course also rewrite the code that uses regular expressions to one that doesn't, but I also think it wise not to introduce multiple variables as a source of error at once.
>
> Some of the responses would be best answered by looking at the expressions and the code that uses them, so here are the two "benchmark" scripts.
>
> Java: https://gist.github.com/3940931
> Perl: https://gist.github.com/3940780
>
> I'm also copying Dongye Meng here, who is a CS student at UNC working with us on the project - if anyone has further wisdom to share about how to reduce the performance gap between the two versions, he'd surely appreciate.
>
>         -hilmar
>
> On Oct 23, 2012, at 6:42 AM, Phillip Lord wrote:
>
>> Hilmar Lapp <hlapp at drycafe.net> writes:
>>> They (at least as in java.util.regex) have been reported to me as
>>> performing much slower (by several orders of magnitude) than the regex
>>> implementation in Perl, and some simple benchmarking tests seem to
>>> bear that out. Even after scrutinizing the benchmark and finding
>>> nothing obvious, I'm still skeptical as to why this would be the case
>>> - naively I would have assumed that the underlying runtime library is
>>> implemented in C in both cases. But perhaps this is not true?
>>
>>
>> Well, the difference is that Perl is perl, while Java is not; it all
>> depends on the JVM, and libraries also. A quick shuftie at
>> the source for the open-jdk libraries suggests that the regexp searching
>> is done in Java -- it's not just a drop through to C. Always the problem
>> with performance optimisation on Java -- you are only optimising for one
>> situation. It might be interesting to see how much variation there is
>> between JVMs.
>>
>> Like others, I would only use regexp as a last resort in Java anyway;
>> compared to Perl, writing the code is painful. Still, I guess that you
>> know this!
>>
>> Phil
>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l



From to.petr at gmail.com  Wed Oct 24 18:30:16 2012
From: to.petr at gmail.com (P. Troshin)
Date: Wed, 24 Oct 2012 19:30:16 +0100
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <CAAT4F8mRXOVvRX9RyMBi1mzB_LPodYK2Z9Q+SiP6=W2q16uMLw@mail.gmail.com>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<874nllo4fx.fsf@newcastle.ac.uk>
	<4F9982AE-FA76-41BF-BF1B-58B7889F03AB@drycafe.net>
	<CAAT4F8mRXOVvRX9RyMBi1mzB_LPodYK2Z9Q+SiP6=W2q16uMLw@mail.gmail.com>
Message-ID: <CAAT4F8kT41E=p5OOn=EgPXdbFnQzOsMHej00Scpt1D2EN+tZ8Q@mail.gmail.com>

Hi Hilmar,

Looked at the test in a bit more details, I can see what you are
trying to test but is there a real life problem behind this?
What this test is doing is a lot of searches on very short strings. Is
this what your real life application does? I am asking because if your
real life application uses regexp to look into long string, the
performance might be totally different.
What is your aim - 3 seconds for 500K searches do not seem
particularly slow to me.

Thanks
Peter


On 24 October 2012 19:10, P. Troshin <to.petr at gmail.com> wrote:
> Hi Hilmar,
>
> Hmm, it looks like I spoke too soon; the previous run was doing
> nothing as all of the cases were commented out.
> I can now see that the results of my runs are not massively different
> from that of yours.
> It would help if you could encourage your student to write a few unit
> tests so that we know what you are trying to achieve and to simplify
> the testing.
>
> Just a thought
>
> Thanks,
> Peter
>
>
>
> On 24 October 2012 17:47, Hilmar Lapp <hlapp at drycafe.net> wrote:
>> Hi everyone,
>>
>> Thanks for all your responses. Indeed I know that the Java regex API isn't an enjoyable one to program with, and if the underlying task were about writing something from scratch, I'd be all for avoiding regex's too if the same thing could be achieved by string comparison.
>>
>> However, and of course I failed to say that initially, the task from which this query is originating is about converting a Perl script to Java (not because Perl is somehow bad, but because those Perl scripts have shown to be an obstacle to easy cross-platform installation of the - mostly Java - software they are a part of). That doesn't mean one couldn't in the course also rewrite the code that uses regular expressions to one that doesn't, but I also think it wise not to introduce multiple variables as a source of error at once.
>>
>> Some of the responses would be best answered by looking at the expressions and the code that uses them, so here are the two "benchmark" scripts.
>>
>> Java: https://gist.github.com/3940931
>> Perl: https://gist.github.com/3940780
>>
>> I'm also copying Dongye Meng here, who is a CS student at UNC working with us on the project - if anyone has further wisdom to share about how to reduce the performance gap between the two versions, he'd surely appreciate.
>>
>>         -hilmar
>>
>> On Oct 23, 2012, at 6:42 AM, Phillip Lord wrote:
>>
>>> Hilmar Lapp <hlapp at drycafe.net> writes:
>>>> They (at least as in java.util.regex) have been reported to me as
>>>> performing much slower (by several orders of magnitude) than the regex
>>>> implementation in Perl, and some simple benchmarking tests seem to
>>>> bear that out. Even after scrutinizing the benchmark and finding
>>>> nothing obvious, I'm still skeptical as to why this would be the case
>>>> - naively I would have assumed that the underlying runtime library is
>>>> implemented in C in both cases. But perhaps this is not true?
>>>
>>>
>>> Well, the difference is that Perl is perl, while Java is not; it all
>>> depends on the JVM, and libraries also. A quick shuftie at
>>> the source for the open-jdk libraries suggests that the regexp searching
>>> is done in Java -- it's not just a drop through to C. Always the problem
>>> with performance optimisation on Java -- you are only optimising for one
>>> situation. It might be interesting to see how much variation there is
>>> between JVMs.
>>>
>>> Like others, I would only use regexp as a last resort in Java anyway;
>>> compared to Perl, writing the code is painful. Still, I guess that you
>>> know this!
>>>
>>> Phil
>>
>> --
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>> ===========================================================
>>
>>
>>
>>
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l



From hlapp at drycafe.net  Thu Oct 25 03:45:52 2012
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 24 Oct 2012 23:45:52 -0400
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <CAAT4F8kT41E=p5OOn=EgPXdbFnQzOsMHej00Scpt1D2EN+tZ8Q@mail.gmail.com>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<874nllo4fx.fsf@newcastle.ac.uk>
	<4F9982AE-FA76-41BF-BF1B-58B7889F03AB@drycafe.net>
	<CAAT4F8mRXOVvRX9RyMBi1mzB_LPodYK2Z9Q+SiP6=W2q16uMLw@mail.gmail.com>
	<CAAT4F8kT41E=p5OOn=EgPXdbFnQzOsMHej00Scpt1D2EN+tZ8Q@mail.gmail.com>
Message-ID: <34DFDF13-5014-4383-A3D3-BAF793AC2E23@drycafe.net>

The code is a very small snippet from a natural language processing software aimed at extracting structured phenotype descriptions from un- or semistructured free text. Apparently the code as is (in Perl) makes a lot of regular expression matches, and so if the speed difference for them between Perl and Java is significant, in theory this might become a problem. Though whether it will or will not amount to a bottleneck indeed remains to be seen, as the code is also doing other things that are potentially expensive, and possibly more so than the regex matching. 

So the exercise here is merely to see whether there is a notable performance difference in regex pattern evaluation that can't simply be attributed to programming mistakes (and apparently there is).

	-hilmar

On Oct 24, 2012, at 2:30 PM, P. Troshin wrote:

> Hi Hilmar,
> 
> Looked at the test in a bit more details, I can see what you are
> trying to test but is there a real life problem behind this?
> What this test is doing is a lot of searches on very short strings. Is
> this what your real life application does? I am asking because if your
> real life application uses regexp to look into long string, the
> performance might be totally different.
> What is your aim - 3 seconds for 500K searches do not seem
> particularly slow to me.
> 
> Thanks
> Peter
> 
> 
> On 24 October 2012 19:10, P. Troshin <to.petr at gmail.com> wrote:
>> Hi Hilmar,
>> 
>> Hmm, it looks like I spoke too soon; the previous run was doing
>> nothing as all of the cases were commented out.
>> I can now see that the results of my runs are not massively different
>> from that of yours.
>> It would help if you could encourage your student to write a few unit
>> tests so that we know what you are trying to achieve and to simplify
>> the testing.
>> 
>> Just a thought
>> 
>> Thanks,
>> Peter
>> 
>> 
>> 
>> On 24 October 2012 17:47, Hilmar Lapp <hlapp at drycafe.net> wrote:
>>> Hi everyone,
>>> 
>>> Thanks for all your responses. Indeed I know that the Java regex API isn't an enjoyable one to program with, and if the underlying task were about writing something from scratch, I'd be all for avoiding regex's too if the same thing could be achieved by string comparison.
>>> 
>>> However, and of course I failed to say that initially, the task from which this query is originating is about converting a Perl script to Java (not because Perl is somehow bad, but because those Perl scripts have shown to be an obstacle to easy cross-platform installation of the - mostly Java - software they are a part of). That doesn't mean one couldn't in the course also rewrite the code that uses regular expressions to one that doesn't, but I also think it wise not to introduce multiple variables as a source of error at once.
>>> 
>>> Some of the responses would be best answered by looking at the expressions and the code that uses them, so here are the two "benchmark" scripts.
>>> 
>>> Java: https://gist.github.com/3940931
>>> Perl: https://gist.github.com/3940780
>>> 
>>> I'm also copying Dongye Meng here, who is a CS student at UNC working with us on the project - if anyone has further wisdom to share about how to reduce the performance gap between the two versions, he'd surely appreciate.
>>> 
>>>        -hilmar
>>> 
>>> On Oct 23, 2012, at 6:42 AM, Phillip Lord wrote:
>>> 
>>>> Hilmar Lapp <hlapp at drycafe.net> writes:
>>>>> They (at least as in java.util.regex) have been reported to me as
>>>>> performing much slower (by several orders of magnitude) than the regex
>>>>> implementation in Perl, and some simple benchmarking tests seem to
>>>>> bear that out. Even after scrutinizing the benchmark and finding
>>>>> nothing obvious, I'm still skeptical as to why this would be the case
>>>>> - naively I would have assumed that the underlying runtime library is
>>>>> implemented in C in both cases. But perhaps this is not true?
>>>> 
>>>> 
>>>> Well, the difference is that Perl is perl, while Java is not; it all
>>>> depends on the JVM, and libraries also. A quick shuftie at
>>>> the source for the open-jdk libraries suggests that the regexp searching
>>>> is done in Java -- it's not just a drop through to C. Always the problem
>>>> with performance optimisation on Java -- you are only optimising for one
>>>> situation. It might be interesting to see how much variation there is
>>>> between JVMs.
>>>> 
>>>> Like others, I would only use regexp as a last resort in Java anyway;
>>>> compared to Perl, writing the code is painful. Still, I guess that you
>>>> know this!
>>>> 
>>>> Phil
>>> 
>>> --
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> ===========================================================
>>> 
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================







From daniel.quest at gmail.com  Thu Oct 25 03:51:53 2012
From: daniel.quest at gmail.com (daniel.quest at gmail.com)
Date: Wed, 24 Oct 2012 22:51:53 -0500
Subject: [Biojava-l] regex performance in Java
In-Reply-To: <34DFDF13-5014-4383-A3D3-BAF793AC2E23@drycafe.net>
References: <1B62BC3E-B005-4484-AE66-0B8F407E4756@drycafe.net>
	<874nllo4fx.fsf@newcastle.ac.uk>
	<4F9982AE-FA76-41BF-BF1B-58B7889F03AB@drycafe.net>
	<CAAT4F8mRXOVvRX9RyMBi1mzB_LPodYK2Z9Q+SiP6=W2q16uMLw@mail.gmail.com>
	<CAAT4F8kT41E=p5OOn=EgPXdbFnQzOsMHej00Scpt1D2EN+tZ8Q@mail.gmail.com>
	<34DFDF13-5014-4383-A3D3-BAF793AC2E23@drycafe.net>
Message-ID: <AC1E9496-7603-4F55-A8BB-818DD1CD7786@gmail.com>

Have you ever used uima?  Same software used on the IBM Watson project.  Very very powerful.

http://uima.apache.org/

Dan

Sent from my iPhone

On Oct 24, 2012, at 10:45 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> The code is a very small snippet from a natural language processing software aimed at extracting structured phenotype descriptions from un- or semistructured free text. Apparently the code as is (in Perl) makes a lot of regular expression matches, and so if the speed difference for them between Perl and Java is significant, in theory this might become a problem. Though whether it will or will not amount to a bottleneck indeed remains to be seen, as the code is also doing other things that are potentially expensive, and possibly more so than the regex matching. 
> 
> So the exercise here is merely to see whether there is a notable performance difference in regex pattern evaluation that can't simply be attributed to programming mistakes (and apparently there is).
> 
>    -hilmar
> 
> On Oct 24, 2012, at 2:30 PM, P. Troshin wrote:
> 
>> Hi Hilmar,
>> 
>> Looked at the test in a bit more details, I can see what you are
>> trying to test but is there a real life problem behind this?
>> What this test is doing is a lot of searches on very short strings. Is
>> this what your real life application does? I am asking because if your
>> real life application uses regexp to look into long string, the
>> performance might be totally different.
>> What is your aim - 3 seconds for 500K searches do not seem
>> particularly slow to me.
>> 
>> Thanks
>> Peter
>> 
>> 
>> On 24 October 2012 19:10, P. Troshin <to.petr at gmail.com> wrote:
>>> Hi Hilmar,
>>> 
>>> Hmm, it looks like I spoke too soon; the previous run was doing
>>> nothing as all of the cases were commented out.
>>> I can now see that the results of my runs are not massively different
>>> from that of yours.
>>> It would help if you could encourage your student to write a few unit
>>> tests so that we know what you are trying to achieve and to simplify
>>> the testing.
>>> 
>>> Just a thought
>>> 
>>> Thanks,
>>> Peter
>>> 
>>> 
>>> 
>>> On 24 October 2012 17:47, Hilmar Lapp <hlapp at drycafe.net> wrote:
>>>> Hi everyone,
>>>> 
>>>> Thanks for all your responses. Indeed I know that the Java regex API isn't an enjoyable one to program with, and if the underlying task were about writing something from scratch, I'd be all for avoiding regex's too if the same thing could be achieved by string comparison.
>>>> 
>>>> However, and of course I failed to say that initially, the task from which this query is originating is about converting a Perl script to Java (not because Perl is somehow bad, but because those Perl scripts have shown to be an obstacle to easy cross-platform installation of the - mostly Java - software they are a part of). That doesn't mean one couldn't in the course also rewrite the code that uses regular expressions to one that doesn't, but I also think it wise not to introduce multiple variables as a source of error at once.
>>>> 
>>>> Some of the responses would be best answered by looking at the expressions and the code that uses them, so here are the two "benchmark" scripts.
>>>> 
>>>> Java: https://gist.github.com/3940931
>>>> Perl: https://gist.github.com/3940780
>>>> 
>>>> I'm also copying Dongye Meng here, who is a CS student at UNC working with us on the project - if anyone has further wisdom to share about how to reduce the performance gap between the two versions, he'd surely appreciate.
>>>> 
>>>>       -hilmar
>>>> 
>>>> On Oct 23, 2012, at 6:42 AM, Phillip Lord wrote:
>>>> 
>>>>> Hilmar Lapp <hlapp at drycafe.net> writes:
>>>>>> They (at least as in java.util.regex) have been reported to me as
>>>>>> performing much slower (by several orders of magnitude) than the regex
>>>>>> implementation in Perl, and some simple benchmarking tests seem to
>>>>>> bear that out. Even after scrutinizing the benchmark and finding
>>>>>> nothing obvious, I'm still skeptical as to why this would be the case
>>>>>> - naively I would have assumed that the underlying runtime library is
>>>>>> implemented in C in both cases. But perhaps this is not true?
>>>>> 
>>>>> 
>>>>> Well, the difference is that Perl is perl, while Java is not; it all
>>>>> depends on the JVM, and libraries also. A quick shuftie at
>>>>> the source for the open-jdk libraries suggests that the regexp searching
>>>>> is done in Java -- it's not just a drop through to C. Always the problem
>>>>> with performance optimisation on Java -- you are only optimising for one
>>>>> situation. It might be interesting to see how much variation there is
>>>>> between JVMs.
>>>>> 
>>>>> Like others, I would only use regexp as a last resort in Java anyway;
>>>>> compared to Perl, writing the code is painful. Still, I guess that you
>>>>> know this!
>>>>> 
>>>>> Phil
>>>> 
>>>> --
>>>> ===========================================================
>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>>> ===========================================================
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l



From andreas at sdsc.edu  Wed Oct 31 20:48:07 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 31 Oct 2012 13:48:07 -0700
Subject: [Biojava-l] open-bio servers moving
Message-ID: <CALthepw=Suuw8XU+xJJ==X5tZ-V_fAiritxeW-zkxra22y2Hqg@mail.gmail.com>

Hi,

The portal.open-bio.org server that is hosting the biojava wiki site is
currently down, since it is being moved to a new location on the Amazon
Cloud.

It may take a few days until everything has been set up properly and the
wiki will be back.

If there is anybody on the biojava side who wants to join the open
bioinformatics foundation's sysadmin team and help out with projects like
this one, this would be a good moment to volunteer...

Andreas