From andreas at sdsc.edu  Wed Jul 18 14:01:30 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 18 Jul 2012 11:01:30 -0700
Subject: [Biojava-l] biojava Chain
In-Reply-To: <CAKe9EA8aN=PZtj+VROXSbesh99yFRwk6LaB9dEF1kDupgrybNQ@mail.gmail.com>
References: <CAKe9EA8aN=PZtj+VROXSbesh99yFRwk6LaB9dEF1kDupgrybNQ@mail.gmail.com>
Message-ID: <CALthepwL7p2i52RrMGT1Exp3Zuz5nqfA0Sf2iG4UWbAdeZjRcg@mail.gmail.com>

Hi Jian,

please don't send support emails to me directly but to the list. Chances
are that somebody else can respond faster than me, or that other users are
struggling with the same problem...

To answer your question, are you running with the "alignSeqRes" parameter
set to true?

The code below should do the job...

Andreas

AtomCache cache = new AtomCache();

 cache.getFileParsingParams().setAlignSeqRes(true);

 Structure struc = cache.getStructure("1fnt");

 System.out.println(struc);


On Tue, Jul 17, 2012 at 4:05 PM, Jian Wang <bugouzhi at gmail.com> wrote:

> Hi Andrea:
> I have a quick question regarding the Chain object in biojava3, since
> it listed you as the author in javadoc :-)...
> After loading a structure from a pdb file... I can assess the residue
> using getAtomGroup() and related methods but if i try to use the
> getSeqResGroup() and methods related to the SEQRES, everything
> is empty... the particular pdb file i loaded is 1FNT. The reason i need the
> SEQRES is because i try to assess certain atoms according to its index
> in the original sequence and the getAtomGroup() method will sometime fail
> when
> missing data are in the pdb file... any idea? thanks a lot
>
>
>
>
>
>
>
>
>
>
>
> cheers
>
>
>
> Jian
>

From power3d at gmail.com  Tue Jul 24 06:09:09 2012
From: power3d at gmail.com (Tony Power)
Date: Tue, 24 Jul 2012 11:09:09 +0100
Subject: [Biojava-l] error on hmmer demo
Message-ID: <CAMNg4Hjb5+XKXKFtaCiN=UB9BQ2PnodYPt2fO7pO6bzRLcFY9Q@mail.gmail.com>

Hi all,

When I am trying to run the demo at:
http://biojava.org/wiki/BioJava:CookBook3:HmmerService

I get the following error:

java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.Integer
#	         Domain	       ACC	Start	End	  eValue	Description
	at org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:119)
	at org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:42)

I have BioJava 3.0.4.

Thanks,
Tony

From andreas at sdsc.edu  Tue Jul 24 11:19:05 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 24 Jul 2012 08:19:05 -0700
Subject: [Biojava-l] error on hmmer demo
In-Reply-To: <CAMNg4Hjb5+XKXKFtaCiN=UB9BQ2PnodYPt2fO7pO6bzRLcFY9Q@mail.gmail.com>
References: <CAMNg4Hjb5+XKXKFtaCiN=UB9BQ2PnodYPt2fO7pO6bzRLcFY9Q@mail.gmail.com>
Message-ID: <CALthepx_JDeZYU+K6x-b9OYWAJivw+m+fKhJavscqW1oAYBU=g@mail.gmail.com>

Thanks for the feedback. It works in my environments, but it might have to
do with the conversion of JSON->Java object.

- How did you get your biojava setup? Maven? manually?
- If manual setup, are you using net.sf.json-lib v. 2.3?
- What is your operating system and java version?

Thanks,

Andreas


On Tue, Jul 24, 2012 at 3:09 AM, Tony Power <power3d at gmail.com> wrote:

> Hi all,
>
> When I am trying to run the demo at:
> http://biojava.org/wiki/BioJava:CookBook3:HmmerService
>
> I get the following error:
>
> java.lang.ClassCastException: java.lang.Long cannot be cast to
> java.lang.Integer
> #                Domain        ACC      Start   End       eValue
>  Description
>         at
> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:119)
>         at
> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:42)
>
> I have BioJava 3.0.4.
>
> Thanks,
> Tony
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From akallu at ncmir.ucsd.edu  Mon Jul 23 18:15:29 2012
From: akallu at ncmir.ucsd.edu (Amritpal Kallu)
Date: Mon, 23 Jul 2012 15:15:29 -0700
Subject: [Biojava-l] Interested in working on BioJava
Message-ID: <500DCD01.2010108@ncmir.ucsd.edu>

Hello all,

I am 4th year undergraduate at University of California, San Diego. I am 
extremely interested in being of some help on the BioJava project. 
Unfortunately I have never worked on an open source project, so I 
imagine I will have somewhat of a learning curve to encounter. I have 
attached my resume, and I would be happy to work on whatever is needed / 
works best with my particular skillset. Thank you again for your time, 
and I look forward to being of some use to this awesome project!
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From andreas at sdsc.edu  Tue Jul 24 12:08:36 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 24 Jul 2012 09:08:36 -0700
Subject: [Biojava-l] Interested in working on BioJava
In-Reply-To: <500DCD01.2010108@ncmir.ucsd.edu>
References: <500DCD01.2010108@ncmir.ucsd.edu>
Message-ID: <CALthepywT7=3U8=G1Nx=svTRwcSmnPpSxXhh4ER6WBEdL+bp2g@mail.gmail.com>

Hi Amritpal,

great to see you are interested. It is probably best to start with a
checkout of the source code and run some of the cookbook-examples.
That should give you a feeling what particular aspects of the project
you are interested in... Once you are at that stage we can discuss
more...

Andreas



On Mon, Jul 23, 2012 at 3:15 PM, Amritpal Kallu <akallu at ncmir.ucsd.edu> wrote:
> Hello all,
>
> I am 4th year undergraduate at University of California, San Diego. I am
> extremely interested in being of some help on the BioJava project.
> Unfortunately I have never worked on an open source project, so I imagine I
> will have somewhat of a learning curve to encounter. I have attached my
> resume, and I would be happy to work on whatever is needed / works best with
> my particular skillset. Thank you again for your time, and I look forward to
> being of some use to this awesome project!
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From power3d at gmail.com  Tue Jul 24 12:15:40 2012
From: power3d at gmail.com (Tony Power)
Date: Tue, 24 Jul 2012 17:15:40 +0100
Subject: [Biojava-l] error on hmmer demo
In-Reply-To: <CALthepx_JDeZYU+K6x-b9OYWAJivw+m+fKhJavscqW1oAYBU=g@mail.gmail.com>
References: <CAMNg4Hjb5+XKXKFtaCiN=UB9BQ2PnodYPt2fO7pO6bzRLcFY9Q@mail.gmail.com>
	<CALthepx_JDeZYU+K6x-b9OYWAJivw+m+fKhJavscqW1oAYBU=g@mail.gmail.com>
Message-ID: <CAMNg4HgthUGSyqr-OmKhzMh3ARTr7dMKcrvWWKkgoLu=sj6rEg@mail.gmail.com>

Hi again,

Sorry about the lack of details.
Here it goes:
Debian testing;
Biojava from debian repository;
OpenJDK 7 (installed from debian rep too);

Thanks,

On Tue, Jul 24, 2012 at 4:19 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Thanks for the feedback. It works in my environments, but it might have to
> do with the conversion of JSON->Java object.
>
> - How did you get your biojava setup? Maven? manually?
> - If manual setup, are you using net.sf.json-lib v. 2.3?
> - What is your operating system and java version?
>
> Thanks,
>
> Andreas
>
>
> On Tue, Jul 24, 2012 at 3:09 AM, Tony Power <power3d at gmail.com> wrote:
>>
>> Hi all,
>>
>> When I am trying to run the demo at:
>> http://biojava.org/wiki/BioJava:CookBook3:HmmerService
>>
>> I get the following error:
>>
>> java.lang.ClassCastException: java.lang.Long cannot be cast to
>> java.lang.Integer
>> #                Domain        ACC      Start   End       eValue
>> Description
>>         at
>> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:119)
>>         at
>> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:42)
>>
>> I have BioJava 3.0.4.
>>
>> Thanks,
>> Tony
>> _______________________________________________
>> 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  Tue Jul 24 12:19:50 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 24 Jul 2012 09:19:50 -0700
Subject: [Biojava-l] error on hmmer demo
In-Reply-To: <CAMNg4HgthUGSyqr-OmKhzMh3ARTr7dMKcrvWWKkgoLu=sj6rEg@mail.gmail.com>
References: <CAMNg4Hjb5+XKXKFtaCiN=UB9BQ2PnodYPt2fO7pO6bzRLcFY9Q@mail.gmail.com>
	<CALthepx_JDeZYU+K6x-b9OYWAJivw+m+fKhJavscqW1oAYBU=g@mail.gmail.com>
	<CAMNg4HgthUGSyqr-OmKhzMh3ARTr7dMKcrvWWKkgoLu=sj6rEg@mail.gmail.com>
Message-ID: <CALthepziSnnPr5f1WOGtaFsPU2VqQHhuqXHqGDkoqQNsCVw59A@mail.gmail.com>

Can you try with sun-java, rather than openjdk?
A

On Tue, Jul 24, 2012 at 9:15 AM, Tony Power <power3d at gmail.com> wrote:
> Hi again,
>
> Sorry about the lack of details.
> Here it goes:
> Debian testing;
> Biojava from debian repository;
> OpenJDK 7 (installed from debian rep too);
>
> Thanks,
>
> On Tue, Jul 24, 2012 at 4:19 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> Thanks for the feedback. It works in my environments, but it might have to
>> do with the conversion of JSON->Java object.
>>
>> - How did you get your biojava setup? Maven? manually?
>> - If manual setup, are you using net.sf.json-lib v. 2.3?
>> - What is your operating system and java version?
>>
>> Thanks,
>>
>> Andreas
>>
>>
>> On Tue, Jul 24, 2012 at 3:09 AM, Tony Power <power3d at gmail.com> wrote:
>>>
>>> Hi all,
>>>
>>> When I am trying to run the demo at:
>>> http://biojava.org/wiki/BioJava:CookBook3:HmmerService
>>>
>>> I get the following error:
>>>
>>> java.lang.ClassCastException: java.lang.Long cannot be cast to
>>> java.lang.Integer
>>> #                Domain        ACC      Start   End       eValue
>>> Description
>>>         at
>>> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:119)
>>>         at
>>> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:42)
>>>
>>> I have BioJava 3.0.4.
>>>
>>> Thanks,
>>> Tony
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>
>>

From power3d at gmail.com  Wed Jul 25 06:15:33 2012
From: power3d at gmail.com (Tony Power)
Date: Wed, 25 Jul 2012 11:15:33 +0100
Subject: [Biojava-l] error on hmmer demo
In-Reply-To: <CALthepziSnnPr5f1WOGtaFsPU2VqQHhuqXHqGDkoqQNsCVw59A@mail.gmail.com>
References: <CAMNg4Hjb5+XKXKFtaCiN=UB9BQ2PnodYPt2fO7pO6bzRLcFY9Q@mail.gmail.com>
	<CALthepx_JDeZYU+K6x-b9OYWAJivw+m+fKhJavscqW1oAYBU=g@mail.gmail.com>
	<CAMNg4HgthUGSyqr-OmKhzMh3ARTr7dMKcrvWWKkgoLu=sj6rEg@mail.gmail.com>
	<CALthepziSnnPr5f1WOGtaFsPU2VqQHhuqXHqGDkoqQNsCVw59A@mail.gmail.com>
Message-ID: <CAMNg4HjNjVi5OXHbeT966Lc++CC3KXFTT133NgO2j96DmUASCw@mail.gmail.com>

HI,

On Mac OSx 10, Sun Java 1.6:

Exception in thread "main" java.lang.NoClassDefFoundError: org/json/JSONObject
	at org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:105)
	at org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:41)
	at biodemo.BioDemo.main(BioDemo.java:37)
Caused by: java.lang.ClassNotFoundException: org.json.JSONObject
	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	... 3 more
Java Result: 1

On Win 7, Java 1.6:

java.net.UnknownHostException: hmmer.janelia.org
        at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:177)
        at java.net.Socket.connect(Socket.java:519)
        at java.net.Socket.connect(Socket.java:469)
        at sun.net.NetworkClient.doConnect(NetworkClient.java:157)
        at sun.net.www.http.HttpClient.openServer(HttpClient.java:394)
        at sun.net.www.http.HttpClient.openServer(HttpClient.java:529)
        at sun.net.www.http.HttpClient.<init>(HttpClient.java:233)
        at sun.net.www.http.HttpClient.New(HttpClient.java:306)
        at sun.net.www.http.HttpClient.New(HttpClient.java:323)
        at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:788)
        at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:729)
        at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:654)
        at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(HttpURLConnection.java:832)
        at org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:69)
        at org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:41)
        at biodemo.BioDemo.main(BioDemo.java:37)

I have Internet connection, for the proteins are successfully
downloaded in any of the three cases.

Thanks,
Tony

On Tue, Jul 24, 2012 at 5:19 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Can you try with sun-java, rather than openjdk?
> A
>
> On Tue, Jul 24, 2012 at 9:15 AM, Tony Power <power3d at gmail.com> wrote:
>> Hi again,
>>
>> Sorry about the lack of details.
>> Here it goes:
>> Debian testing;
>> Biojava from debian repository;
>> OpenJDK 7 (installed from debian rep too);
>>
>> Thanks,
>>
>> On Tue, Jul 24, 2012 at 4:19 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>> Thanks for the feedback. It works in my environments, but it might have to
>>> do with the conversion of JSON->Java object.
>>>
>>> - How did you get your biojava setup? Maven? manually?
>>> - If manual setup, are you using net.sf.json-lib v. 2.3?
>>> - What is your operating system and java version?
>>>
>>> Thanks,
>>>
>>> Andreas
>>>
>>>
>>> On Tue, Jul 24, 2012 at 3:09 AM, Tony Power <power3d at gmail.com> wrote:
>>>>
>>>> Hi all,
>>>>
>>>> When I am trying to run the demo at:
>>>> http://biojava.org/wiki/BioJava:CookBook3:HmmerService
>>>>
>>>> I get the following error:
>>>>
>>>> java.lang.ClassCastException: java.lang.Long cannot be cast to
>>>> java.lang.Integer
>>>> #                Domain        ACC      Start   End       eValue
>>>> Description
>>>>         at
>>>> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:119)
>>>>         at
>>>> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:42)
>>>>
>>>> I have BioJava 3.0.4.
>>>>
>>>> Thanks,
>>>> Tony
>>>> _______________________________________________
>>>> 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 Jul 25 10:32:39 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 25 Jul 2012 07:32:39 -0700
Subject: [Biojava-l] error on hmmer demo
In-Reply-To: <CAMNg4HjNjVi5OXHbeT966Lc++CC3KXFTT133NgO2j96DmUASCw@mail.gmail.com>
References: <CAMNg4Hjb5+XKXKFtaCiN=UB9BQ2PnodYPt2fO7pO6bzRLcFY9Q@mail.gmail.com>
	<CALthepx_JDeZYU+K6x-b9OYWAJivw+m+fKhJavscqW1oAYBU=g@mail.gmail.com>
	<CAMNg4HgthUGSyqr-OmKhzMh3ARTr7dMKcrvWWKkgoLu=sj6rEg@mail.gmail.com>
	<CALthepziSnnPr5f1WOGtaFsPU2VqQHhuqXHqGDkoqQNsCVw59A@mail.gmail.com>
	<CAMNg4HjNjVi5OXHbeT966Lc++CC3KXFTT133NgO2j96DmUASCw@mail.gmail.com>
Message-ID: <CALthepzn2kCDb0Q3_u5oqw_s_9NY-51-9Qjd6+gkd1tcL5kvng@mail.gmail.com>

Hi Tony,

> On Mac OSx 10, Sun Java 1.6:
> Exception in thread "main" java.lang.NoClassDefFoundError: org/json/JSONObject

depending on your biojava version you need either
net.sf.json-lib or org.json.json
in your classpath. (we switched recently for debian licensing reasons)


> On Win 7, Java 1.6:
> java.net.UnknownHostException: hmmer.janelia.org

networking problems? Definitely is the correct location... Your Osx
setup can get past that stage...

Hope that helps..

Andreas

From andreas at sdsc.edu  Wed Jul 18 18:01:30 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 18 Jul 2012 11:01:30 -0700
Subject: [Biojava-l] biojava Chain
In-Reply-To: <CAKe9EA8aN=PZtj+VROXSbesh99yFRwk6LaB9dEF1kDupgrybNQ@mail.gmail.com>
References: <CAKe9EA8aN=PZtj+VROXSbesh99yFRwk6LaB9dEF1kDupgrybNQ@mail.gmail.com>
Message-ID: <CALthepwL7p2i52RrMGT1Exp3Zuz5nqfA0Sf2iG4UWbAdeZjRcg@mail.gmail.com>

Hi Jian,

please don't send support emails to me directly but to the list. Chances
are that somebody else can respond faster than me, or that other users are
struggling with the same problem...

To answer your question, are you running with the "alignSeqRes" parameter
set to true?

The code below should do the job...

Andreas

AtomCache cache = new AtomCache();

 cache.getFileParsingParams().setAlignSeqRes(true);

 Structure struc = cache.getStructure("1fnt");

 System.out.println(struc);


On Tue, Jul 17, 2012 at 4:05 PM, Jian Wang <bugouzhi at gmail.com> wrote:

> Hi Andrea:
> I have a quick question regarding the Chain object in biojava3, since
> it listed you as the author in javadoc :-)...
> After loading a structure from a pdb file... I can assess the residue
> using getAtomGroup() and related methods but if i try to use the
> getSeqResGroup() and methods related to the SEQRES, everything
> is empty... the particular pdb file i loaded is 1FNT. The reason i need the
> SEQRES is because i try to assess certain atoms according to its index
> in the original sequence and the getAtomGroup() method will sometime fail
> when
> missing data are in the pdb file... any idea? thanks a lot
>
>
>
>
>
>
>
>
>
>
>
> cheers
>
>
>
> Jian
>


From power3d at gmail.com  Tue Jul 24 10:09:09 2012
From: power3d at gmail.com (Tony Power)
Date: Tue, 24 Jul 2012 11:09:09 +0100
Subject: [Biojava-l] error on hmmer demo
Message-ID: <CAMNg4Hjb5+XKXKFtaCiN=UB9BQ2PnodYPt2fO7pO6bzRLcFY9Q@mail.gmail.com>

Hi all,

When I am trying to run the demo at:
http://biojava.org/wiki/BioJava:CookBook3:HmmerService

I get the following error:

java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.Integer
#	         Domain	       ACC	Start	End	  eValue	Description
	at org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:119)
	at org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:42)

I have BioJava 3.0.4.

Thanks,
Tony


From andreas at sdsc.edu  Tue Jul 24 15:19:05 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 24 Jul 2012 08:19:05 -0700
Subject: [Biojava-l] error on hmmer demo
In-Reply-To: <CAMNg4Hjb5+XKXKFtaCiN=UB9BQ2PnodYPt2fO7pO6bzRLcFY9Q@mail.gmail.com>
References: <CAMNg4Hjb5+XKXKFtaCiN=UB9BQ2PnodYPt2fO7pO6bzRLcFY9Q@mail.gmail.com>
Message-ID: <CALthepx_JDeZYU+K6x-b9OYWAJivw+m+fKhJavscqW1oAYBU=g@mail.gmail.com>

Thanks for the feedback. It works in my environments, but it might have to
do with the conversion of JSON->Java object.

- How did you get your biojava setup? Maven? manually?
- If manual setup, are you using net.sf.json-lib v. 2.3?
- What is your operating system and java version?

Thanks,

Andreas


On Tue, Jul 24, 2012 at 3:09 AM, Tony Power <power3d at gmail.com> wrote:

> Hi all,
>
> When I am trying to run the demo at:
> http://biojava.org/wiki/BioJava:CookBook3:HmmerService
>
> I get the following error:
>
> java.lang.ClassCastException: java.lang.Long cannot be cast to
> java.lang.Integer
> #                Domain        ACC      Start   End       eValue
>  Description
>         at
> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:119)
>         at
> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:42)
>
> I have BioJava 3.0.4.
>
> Thanks,
> Tony
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From akallu at ncmir.ucsd.edu  Mon Jul 23 22:15:29 2012
From: akallu at ncmir.ucsd.edu (Amritpal Kallu)
Date: Mon, 23 Jul 2012 15:15:29 -0700
Subject: [Biojava-l] Interested in working on BioJava
Message-ID: <500DCD01.2010108@ncmir.ucsd.edu>

Hello all,

I am 4th year undergraduate at University of California, San Diego. I am 
extremely interested in being of some help on the BioJava project. 
Unfortunately I have never worked on an open source project, so I 
imagine I will have somewhat of a learning curve to encounter. I have 
attached my resume, and I would be happy to work on whatever is needed / 
works best with my particular skillset. Thank you again for your time, 
and I look forward to being of some use to this awesome project!
-------------- next part --------------
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From andreas at sdsc.edu  Tue Jul 24 16:08:36 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 24 Jul 2012 09:08:36 -0700
Subject: [Biojava-l] Interested in working on BioJava
In-Reply-To: <500DCD01.2010108@ncmir.ucsd.edu>
References: <500DCD01.2010108@ncmir.ucsd.edu>
Message-ID: <CALthepywT7=3U8=G1Nx=svTRwcSmnPpSxXhh4ER6WBEdL+bp2g@mail.gmail.com>

Hi Amritpal,

great to see you are interested. It is probably best to start with a
checkout of the source code and run some of the cookbook-examples.
That should give you a feeling what particular aspects of the project
you are interested in... Once you are at that stage we can discuss
more...

Andreas



On Mon, Jul 23, 2012 at 3:15 PM, Amritpal Kallu <akallu at ncmir.ucsd.edu> wrote:
> Hello all,
>
> I am 4th year undergraduate at University of California, San Diego. I am
> extremely interested in being of some help on the BioJava project.
> Unfortunately I have never worked on an open source project, so I imagine I
> will have somewhat of a learning curve to encounter. I have attached my
> resume, and I would be happy to work on whatever is needed / works best with
> my particular skillset. Thank you again for your time, and I look forward to
> being of some use to this awesome project!
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From power3d at gmail.com  Tue Jul 24 16:15:40 2012
From: power3d at gmail.com (Tony Power)
Date: Tue, 24 Jul 2012 17:15:40 +0100
Subject: [Biojava-l] error on hmmer demo
In-Reply-To: <CALthepx_JDeZYU+K6x-b9OYWAJivw+m+fKhJavscqW1oAYBU=g@mail.gmail.com>
References: <CAMNg4Hjb5+XKXKFtaCiN=UB9BQ2PnodYPt2fO7pO6bzRLcFY9Q@mail.gmail.com>
	<CALthepx_JDeZYU+K6x-b9OYWAJivw+m+fKhJavscqW1oAYBU=g@mail.gmail.com>
Message-ID: <CAMNg4HgthUGSyqr-OmKhzMh3ARTr7dMKcrvWWKkgoLu=sj6rEg@mail.gmail.com>

Hi again,

Sorry about the lack of details.
Here it goes:
Debian testing;
Biojava from debian repository;
OpenJDK 7 (installed from debian rep too);

Thanks,

On Tue, Jul 24, 2012 at 4:19 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Thanks for the feedback. It works in my environments, but it might have to
> do with the conversion of JSON->Java object.
>
> - How did you get your biojava setup? Maven? manually?
> - If manual setup, are you using net.sf.json-lib v. 2.3?
> - What is your operating system and java version?
>
> Thanks,
>
> Andreas
>
>
> On Tue, Jul 24, 2012 at 3:09 AM, Tony Power <power3d at gmail.com> wrote:
>>
>> Hi all,
>>
>> When I am trying to run the demo at:
>> http://biojava.org/wiki/BioJava:CookBook3:HmmerService
>>
>> I get the following error:
>>
>> java.lang.ClassCastException: java.lang.Long cannot be cast to
>> java.lang.Integer
>> #                Domain        ACC      Start   End       eValue
>> Description
>>         at
>> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:119)
>>         at
>> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:42)
>>
>> I have BioJava 3.0.4.
>>
>> Thanks,
>> Tony
>> _______________________________________________
>> 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  Tue Jul 24 16:19:50 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 24 Jul 2012 09:19:50 -0700
Subject: [Biojava-l] error on hmmer demo
In-Reply-To: <CAMNg4HgthUGSyqr-OmKhzMh3ARTr7dMKcrvWWKkgoLu=sj6rEg@mail.gmail.com>
References: <CAMNg4Hjb5+XKXKFtaCiN=UB9BQ2PnodYPt2fO7pO6bzRLcFY9Q@mail.gmail.com>
	<CALthepx_JDeZYU+K6x-b9OYWAJivw+m+fKhJavscqW1oAYBU=g@mail.gmail.com>
	<CAMNg4HgthUGSyqr-OmKhzMh3ARTr7dMKcrvWWKkgoLu=sj6rEg@mail.gmail.com>
Message-ID: <CALthepziSnnPr5f1WOGtaFsPU2VqQHhuqXHqGDkoqQNsCVw59A@mail.gmail.com>

Can you try with sun-java, rather than openjdk?
A

On Tue, Jul 24, 2012 at 9:15 AM, Tony Power <power3d at gmail.com> wrote:
> Hi again,
>
> Sorry about the lack of details.
> Here it goes:
> Debian testing;
> Biojava from debian repository;
> OpenJDK 7 (installed from debian rep too);
>
> Thanks,
>
> On Tue, Jul 24, 2012 at 4:19 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> Thanks for the feedback. It works in my environments, but it might have to
>> do with the conversion of JSON->Java object.
>>
>> - How did you get your biojava setup? Maven? manually?
>> - If manual setup, are you using net.sf.json-lib v. 2.3?
>> - What is your operating system and java version?
>>
>> Thanks,
>>
>> Andreas
>>
>>
>> On Tue, Jul 24, 2012 at 3:09 AM, Tony Power <power3d at gmail.com> wrote:
>>>
>>> Hi all,
>>>
>>> When I am trying to run the demo at:
>>> http://biojava.org/wiki/BioJava:CookBook3:HmmerService
>>>
>>> I get the following error:
>>>
>>> java.lang.ClassCastException: java.lang.Long cannot be cast to
>>> java.lang.Integer
>>> #                Domain        ACC      Start   End       eValue
>>> Description
>>>         at
>>> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:119)
>>>         at
>>> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:42)
>>>
>>> I have BioJava 3.0.4.
>>>
>>> Thanks,
>>> Tony
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>
>>


From power3d at gmail.com  Wed Jul 25 10:15:33 2012
From: power3d at gmail.com (Tony Power)
Date: Wed, 25 Jul 2012 11:15:33 +0100
Subject: [Biojava-l] error on hmmer demo
In-Reply-To: <CALthepziSnnPr5f1WOGtaFsPU2VqQHhuqXHqGDkoqQNsCVw59A@mail.gmail.com>
References: <CAMNg4Hjb5+XKXKFtaCiN=UB9BQ2PnodYPt2fO7pO6bzRLcFY9Q@mail.gmail.com>
	<CALthepx_JDeZYU+K6x-b9OYWAJivw+m+fKhJavscqW1oAYBU=g@mail.gmail.com>
	<CAMNg4HgthUGSyqr-OmKhzMh3ARTr7dMKcrvWWKkgoLu=sj6rEg@mail.gmail.com>
	<CALthepziSnnPr5f1WOGtaFsPU2VqQHhuqXHqGDkoqQNsCVw59A@mail.gmail.com>
Message-ID: <CAMNg4HjNjVi5OXHbeT966Lc++CC3KXFTT133NgO2j96DmUASCw@mail.gmail.com>

HI,

On Mac OSx 10, Sun Java 1.6:

Exception in thread "main" java.lang.NoClassDefFoundError: org/json/JSONObject
	at org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:105)
	at org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:41)
	at biodemo.BioDemo.main(BioDemo.java:37)
Caused by: java.lang.ClassNotFoundException: org.json.JSONObject
	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	... 3 more
Java Result: 1

On Win 7, Java 1.6:

java.net.UnknownHostException: hmmer.janelia.org
        at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:177)
        at java.net.Socket.connect(Socket.java:519)
        at java.net.Socket.connect(Socket.java:469)
        at sun.net.NetworkClient.doConnect(NetworkClient.java:157)
        at sun.net.www.http.HttpClient.openServer(HttpClient.java:394)
        at sun.net.www.http.HttpClient.openServer(HttpClient.java:529)
        at sun.net.www.http.HttpClient.<init>(HttpClient.java:233)
        at sun.net.www.http.HttpClient.New(HttpClient.java:306)
        at sun.net.www.http.HttpClient.New(HttpClient.java:323)
        at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:788)
        at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:729)
        at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:654)
        at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(HttpURLConnection.java:832)
        at org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:69)
        at org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:41)
        at biodemo.BioDemo.main(BioDemo.java:37)

I have Internet connection, for the proteins are successfully
downloaded in any of the three cases.

Thanks,
Tony

On Tue, Jul 24, 2012 at 5:19 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Can you try with sun-java, rather than openjdk?
> A
>
> On Tue, Jul 24, 2012 at 9:15 AM, Tony Power <power3d at gmail.com> wrote:
>> Hi again,
>>
>> Sorry about the lack of details.
>> Here it goes:
>> Debian testing;
>> Biojava from debian repository;
>> OpenJDK 7 (installed from debian rep too);
>>
>> Thanks,
>>
>> On Tue, Jul 24, 2012 at 4:19 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>> Thanks for the feedback. It works in my environments, but it might have to
>>> do with the conversion of JSON->Java object.
>>>
>>> - How did you get your biojava setup? Maven? manually?
>>> - If manual setup, are you using net.sf.json-lib v. 2.3?
>>> - What is your operating system and java version?
>>>
>>> Thanks,
>>>
>>> Andreas
>>>
>>>
>>> On Tue, Jul 24, 2012 at 3:09 AM, Tony Power <power3d at gmail.com> wrote:
>>>>
>>>> Hi all,
>>>>
>>>> When I am trying to run the demo at:
>>>> http://biojava.org/wiki/BioJava:CookBook3:HmmerService
>>>>
>>>> I get the following error:
>>>>
>>>> java.lang.ClassCastException: java.lang.Long cannot be cast to
>>>> java.lang.Integer
>>>> #                Domain        ACC      Start   End       eValue
>>>> Description
>>>>         at
>>>> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:119)
>>>>         at
>>>> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:42)
>>>>
>>>> I have BioJava 3.0.4.
>>>>
>>>> Thanks,
>>>> Tony
>>>> _______________________________________________
>>>> 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 Jul 25 14:32:39 2012
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 25 Jul 2012 07:32:39 -0700
Subject: [Biojava-l] error on hmmer demo
In-Reply-To: <CAMNg4HjNjVi5OXHbeT966Lc++CC3KXFTT133NgO2j96DmUASCw@mail.gmail.com>
References: <CAMNg4Hjb5+XKXKFtaCiN=UB9BQ2PnodYPt2fO7pO6bzRLcFY9Q@mail.gmail.com>
	<CALthepx_JDeZYU+K6x-b9OYWAJivw+m+fKhJavscqW1oAYBU=g@mail.gmail.com>
	<CAMNg4HgthUGSyqr-OmKhzMh3ARTr7dMKcrvWWKkgoLu=sj6rEg@mail.gmail.com>
	<CALthepziSnnPr5f1WOGtaFsPU2VqQHhuqXHqGDkoqQNsCVw59A@mail.gmail.com>
	<CAMNg4HjNjVi5OXHbeT966Lc++CC3KXFTT133NgO2j96DmUASCw@mail.gmail.com>
Message-ID: <CALthepzn2kCDb0Q3_u5oqw_s_9NY-51-9Qjd6+gkd1tcL5kvng@mail.gmail.com>

Hi Tony,

> On Mac OSx 10, Sun Java 1.6:
> Exception in thread "main" java.lang.NoClassDefFoundError: org/json/JSONObject

depending on your biojava version you need either
net.sf.json-lib or org.json.json
in your classpath. (we switched recently for debian licensing reasons)


> On Win 7, Java 1.6:
> java.net.UnknownHostException: hmmer.janelia.org

networking problems? Definitely is the correct location... Your Osx
setup can get past that stage...

Hope that helps..

Andreas