Nabble - BioJava

Re: [DAS] DAS workshop 7th-9th April 2010

2009-11-26T13:45:43Z

Hi Jonathan,

Any chance it can be webcasted? I'm sure it would attract a lot of
remote attendees ;)

Regards,
Mauricio.

Jonathan Warren wrote:

> We are considering running a Distributed Annotation System workshop here
> at the Sanger/EBI in the UK subject to decent demand.
> The workshop will be held from Wednesday 7th-Friday 9th April 2010. If
> you would be interested in attending either to present or just take part
> then please email me jw12@...
>
> The format of the workshop is likely to be similar to last years (1st
> day for beginners, 2nd for both beginners and advanced users, 3rd day
> for advanced), information for which can be found here:
> http://www.dasregistry.org/course.jsp
>
> If you would like to present then please send a short summary of what
> you would like to talk about.
>
> Thanks
>
> Jonathan.
>
> Jonathan Warren
> Senior Developer and DAS coordinator
> jw12@...
>
>
>
>
>
>
>
>
>

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DAS workshop 7th-9th April 2010

2009-11-26T06:57:35Z

We are considering running a Distributed Annotation System workshop
here at the Sanger/EBI in the UK subject to decent demand.
The workshop will be held from Wednesday 7th-Friday 9th April 2010. If
you would be interested in attending either to present or just take part
then please email me jw12@...

The format of the workshop is likely to be similar to last years (1st
day for beginners, 2nd for both beginners and advanced users, 3rd day
for advanced), information for which can be found here:
http://www.dasregistry.org/course.jsp

If you would like to present then please send a short summary of what
you would like to talk about.

Thanks

Jonathan.

Jonathan Warren
Senior Developer and DAS coordinator
jw12@...

--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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Re: [Biojava-dev] Hackathon in January

2009-11-25T12:08:33Z

I was thinking about video... I would expect that some of the
participants will do some sort of tweeting, blogging, etc.

Andreas

On Wed, Nov 25, 2009 at 4:51 AM, Andy Yates <ayates@...> wrote:

> By online stream do you mean Wave or Twitter or something else trendy? :)
>
> Andy
>
> On 24 Nov 2009, at 17:54, Andreas Prlic wrote:
>
>> * Is anybody interested in following the ongoings at the hackaton via
>> an online-stream? - I received a request about this and am wondering
>> if more people would be interested in this.
>>
>> * Just to repeat the current status regarding the program: So far the
>> plan is to continue working on the new modules. Ideally we will have a
>> brand new biojava 3 ready soon after the hackaton. A more detailed
>> program for the week will be sent out in January.
>>
>> If anybody wants to propose feature requests, you can have a look at
>> the current todo list for the modules:
>> http://biojava.org/wiki/BioJava:Modules
>>
>> Andreas
>>
>>
>>
>> On Tue, Nov 24, 2009 at 7:27 AM, Richard Holland
>> <holland@...> wrote:
>>>
>>> Hi all.
>>>
>>> To anyone planning on attending the BioJava hackathon in Cambridge (UK)
>>> in January, now would be a good time to sort out travel arrangements. If
>>> you're intending to come but haven't yet said so, please do let me know so
>>> that I can ensure we get a big enough room to work in!
>>>
>>> cheers,
>>> Richard
>>>
>>> --
>>> Richard Holland, BSc MBCS
>>> Operations and Delivery Director, Eagle Genomics Ltd
>>> T: +44 (0)1223 654481 ext 3 | E: holland@...
>>> http://www.eaglegenomics.com/
>>>
>>>
>>> _______________________________________________
>>> Biojava-l mailing list - Biojava-l@...
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev@...
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>

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Re: [Biojava-dev] Hackathon in January

2009-11-25T04:51:23Z

By online stream do you mean Wave or Twitter or something else
trendy? :)

Andy

On 24 Nov 2009, at 17:54, Andreas Prlic wrote:

> * Is anybody interested in following the ongoings at the hackaton via
> an online-stream? - I received a request about this and am wondering
> if more people would be interested in this.
>
> * Just to repeat the current status regarding the program: So far the
> plan is to continue working on the new modules. Ideally we will have a
> brand new biojava 3 ready soon after the hackaton. A more detailed
> program for the week will be sent out in January.
>
> If anybody wants to propose feature requests, you can have a look at
> the current todo list for the modules:
> http://biojava.org/wiki/BioJava:Modules
>
> Andreas
>
>
>
> On Tue, Nov 24, 2009 at 7:27 AM, Richard Holland
> <holland@...> wrote:
>> Hi all.
>>
>> To anyone planning on attending the BioJava hackathon in Cambridge
>> (UK) in January, now would be a good time to sort out travel
>> arrangements. If you're intending to come but haven't yet said so,
>> please do let me know so that I can ensure we get a big enough room
>> to work in!
>>
>> cheers,
>> Richard
>>
>> --
>> Richard Holland, BSc MBCS
>> Operations and Delivery Director, Eagle Genomics Ltd
>> T: +44 (0)1223 654481 ext 3 | E: holland@...
>> http://www.eaglegenomics.com/
>>
>>
>> _______________________________________________
>> Biojava-l mailing list - Biojava-l@...
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev@...
> http://lists.open-bio.org/mailman/listinfo/biojava-dev

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Re: Hackathon in January

2009-11-24T09:54:38Z

* Is anybody interested in following the ongoings at the hackaton via
an online-stream? - I received a request about this and am wondering
if more people would be interested in this.

* Just to repeat the current status regarding the program: So far the
plan is to continue working on the new modules. Ideally we will have a
brand new biojava 3 ready soon after the hackaton. A more detailed
program for the week will be sent out in January.

If anybody wants to propose feature requests, you can have a look at
the current todo list for the modules:
http://biojava.org/wiki/BioJava:Modules

Andreas

On Tue, Nov 24, 2009 at 7:27 AM, Richard Holland
<holland@...> wrote:

> Hi all.
>
> To anyone planning on attending the BioJava hackathon in Cambridge (UK) in January, now would be a good time to sort out travel arrangements. If you're intending to come but haven't yet said so, please do let me know so that I can ensure we get a big enough room to work in!
>
> cheers,
> Richard
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland@...
> http://www.eaglegenomics.com/
>
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@...
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

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Hackathon in January

2009-11-24T07:27:20Z

Hi all.

To anyone planning on attending the BioJava hackathon in Cambridge (UK) in January, now would be a good time to sort out travel arrangements. If you're intending to come but haven't yet said so, please do let me know so that I can ensure we get a big enough room to work in!

cheers,
Richard

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland@...
http://www.eaglegenomics.com/

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Fwd: Java Error:- XML Parsing Error: XML or text declaration not at start of entity

2009-11-24T06:51:49Z

Jitesh - I forwarded your response to the list so that everyone can get the chance to reply.

cheers,
Richard

Begin forwarded message:

> From: jitesh dundas <jbdundas@...>
> Date: 24 November 2009 14:47:00 GMT
> To: Richard Holland <holland@...>
> Subject: Re: [Biojava-l] Java Error:- XML Parsing Error: XML or text declaration not at start of entity
>
> Dear Sir,
>
> Thank you for your reply. I figured this problem out by sending records in small sets. e.g. 20 pages per page.
>
> It is like a pagination functionality. For each new page, we need to hit the URl..
>
> My functionality is working fine.I will be happy to share my code with you (and anyone) who needs it.
>
> I simply fetch data from the URL and write to an XML file. Next I just read the XML file and show them in the web page to the user.
>
> Again, I need to know how to fetch records for protein database. Two types of searches are needed I suspect.
>
> First we use the Esearch utility and then the Efetch utility to get the data of the specific protein..
>
> I welcome any suggestions on this !
>
> Thank you everyone for your help.
>
> Regards,
> Jitesh Dundas
>
> On 11/24/09, Richard Holland <holland@...> wrote:
> Your program takes an input 'txtURLString' - could you give an example of the value that this usually contains? I suspect that this URL is where your problem lies but without seeing an example value I couldn't say for sure.
>
> thanks,
> Richard
>
> On 8 Nov 2009, at 10:22, jitesh dundas wrote:
>
> > Dear Sir,
> >
> > My program is working fine and can send me an xml file with 20
> > records. However, it does not allow me to send large amounts of
> > records.
> >
> > For e.g. if I enter "cancer" it will return only 20 records.
> >
> > Can you please tell me what I should do next to get all those records.
> > Thank you in advance
> >
> > Regards,
> > Jitesh Dundas
> >
> > On Sun, Nov 1, 2009 at 9:36 PM, Andreas Prlic <andreas@...> wrote:
> >>
> >> Hi Jitesh,
> >>
> >> It is hard to read your code with all the formatting off probably due to email and many commented lines that don;t seem to get used. Can you provide the stacktrace, so we can see what part of biojava is affected?
> >>
> >> Probably a good strategy to write and debug this is to simply the problem into smaller steps. Try to first download the files you want to parse and write the code to parse them from the local file. That will avoid any issues you might encounter with networking and server/client communication. Once the parsing is working you could take it to the next step and add the server communication...
> >>
> >> Andreas
> >>
> >>
> >>
> >>
> >> On Sun, Nov 1, 2009 at 7:41 AM, jitesh dundas <jbdundas@...> wrote:
> >>>
> >>> Hi friends,
> >>>
> >>> I am getting this error on doing a post(using the code below) to this url->
> >>> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer&reldate=10
> >>>
> >>> I have written this code in .jsp file. Later I will change it into servlet.
> >>>
> >>> Error:-
> >>> XML Parsing Error: XML or text declaration not at start of entity
> >>> Location:
> >>> http://localhost:8080/ProteomDb/ImportFromPubmed2.jsp?txtDbName=pubmed&txtTerm=cancer&txtreldate=10&comSDay=01&comSMonth=01&txtSYear=&comEDay=01&comEMonth=01&txtEYear=&txtURLString=http%3A%2F%2Feutils.ncbi.nlm.nih.gov%2Fentrez%2Feutils%2Fesearch.fcgi%3Fdb%3Dpubmed%26term%3Dcancer%26reldate%3D10&txtsubmit=Fetch+Data+From+NCBI
> >>> Line Number 11, Column 1:<?xml version="1.0" ?><!DOCTYPE eSearchResult
> >>> PUBLIC "-//NLM//DTD eSearchResult, 11 May 2002//EN" "
> >>> http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd"><eSearchResult><Count>2034</Count><RetMax>20</RetMax><RetStart>0</RetStart><IdList>
> >>> <Id>19877350</Id> <Id>19877304</Id> <Id>19877297</Id>
> >>> <Id>19877284</Id> <Id>19877271</Id> <Id>19877265</Id>
> >>> <Id>19877250</Id> <Id>19877245</Id> <Id>19877226</Id>
> >>> <Id>19877210</Id> <Id>19877179</Id> <Id>19877175</Id>
> >>> <Id>19877161</Id> <Id>19877159</Id> <Id>19877158</Id>
> >>> <Id>19877123</Id> <Id>19877122</Id> <Id>19877120</Id>
> >>> <Id>19877119</Id> <Id>19877118</Id>
> >>> </IdList><TranslationSet><Translation> <From>cancer</From>
> >>> <To>"neoplasms"[MeSH Terms] OR "neoplasms"[All Fields] OR "cancer"[All
> >>> Fields]</To> </Translation></TranslationSet><TranslationStack>
> >>> <TermSet> <Term>"neoplasms"[MeSH Terms]</Term> <Field>MeSH
> >>> Terms</Field> <Count>2082133</Count> <Explode>Y</Explode>
> >>> </TermSet> <TermSet> <Term>"neoplasms"[All Fields]</Term> <Field>All
> >>> Fields</Field> <Count>1634731</Count> <Explode>Y</Explode>
> >>> </TermSet> <OP>OR</OP> <TermSet> <Term>"cancer"[All Fields]</Term>
> >>> <Field>All Fields</Field> <Count>902537</Count> <Explode>Y</Explode>
> >>> </TermSet> <OP>OR</OP> <OP>GROUP</OP> <TermSet>
> >>> <Term>2009/10/22[EDAT]</Term> <Field>EDAT</Field> <Count>0</Count>
> >>> <Explode>Y</Explode> </TermSet> <TermSet>
> >>> <Term>2009/11/01[EDAT]</Term> <Field>EDAT</Field> <Count>0</Count>
> >>> <Explode>Y</Explode> </TermSet> <OP>RANGE</OP> <OP>AND</OP>
> >>> </TranslationStack><QueryTranslation>("neoplasms"[MeSH Terms] OR
> >>> "neoplasms"[All Fields] OR "cancer"[All Fields]) AND 2009/10/22[EDAT] :
> >>> 2009/11/01[EDAT]</QueryTranslation></eSearchResult>
> >>> ^
> >>>
> >>> As you can see, the XML output is coming fine but the above error does not
> >>> go..The output via this program should be just like hitting manually the
> >>> above URL in the browser..
> >>> The browser is Mozilla Firefox.
> >>>
> >>> Code:-
> >>>
> >>> <%@ page language = "java" %>
> >>> <%@ page import = "java.sql.*" %>
> >>> <%@ page import = "java.util.*" %>
> >>> <%@ page import = "java.io.*" %>
> >>> <%@ page import="java.lang.*" %>
> >>> <%@ page import="java.net.*" %>
> >>> <%@ page import="java.nio.*" %>
> >>> <%@ page contentType="text/xml; charset=utf-8" pageEncoding="UTF-8" %>
> >>>
> >>>
> >>> <%
> >>>
> >>> try
> >>> {
> >>> //String str = "<?xml version='1.0' ?>";
> >>> //out.println("<?xml version='1.0' encoding='utf-8' ?>");
> >>>
> >>> Properties systemSettings = System.getProperties();
> >>> systemSettings.put("http.proxyHost", "********");
> >>> systemSettings.put("http.proxyPort", "******");
> >>> systemSettings.put("sun.net.client.defaultConnectTimeout", "10000");
> >>> systemSettings.put("sun.net.client.defaultReadTimeout", "10000");
> >>>
> >>> //out.println("Properties Set");
> >>> Authenticator.setDefault(new Authenticator()
> >>> {
> >>> protected PasswordAuthentication getPasswordAuthentication()
> >>> {
> >>> return new PasswordAuthentication("**",
> >>> "******".toCharArray()); // specify ur user name password of iitb login
> >>> }
> >>> });
> >>>
> >>>
> >>> System.setProperties(systemSettings);
> >>> //out.println("After Authentication & Properties Settings");
> >>>
> >>> //create xml file.
> >>> //the input to google api
> >>> //String textAreaContent = request.getParameter("text");
> >>> String textAreaContent = "This si a tst";
> >>>
> >>> String str = "<?xml version='1.0' encoding='utf-8' ?>";
> >>>
> >>> //xml file generation ends here..
> >>> //FetchDataFromNCBI_URLString.jsp
> >>> String URLString = request.getParameter("txtURLString").trim();
> >>>
> >>> //URL url = new URL("
> >>> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=protein&term=BAA20519
> >>> ");
> >>> URL url = new URL(URLString); //url string taken from user input.
> >>> HttpURLConnection connection = null;
> >>>
> >>> connection = (HttpURLConnection) url.openConnection();
> >>> System.out.println("After open connection");
> >>> connection.setRequestMethod("POST");
> >>> connection.setDoInput(true);
> >>> connection.setDoOutput(true);
> >>>
> >>> connection.setUseCaches(false);
> >>> connection.setAllowUserInteraction(false);
> >>> //connection.setFollowRedirects(true);
> >>> //connection.setInstanceFollowRedirects(true);
> >>> //System.out.println("Before-------------------");
> >>> connection.setRequestProperty ("Content-Type","text/xml;
> >>> charset=\"utf-8\"");
> >>> //System.out.println("After-------------------");
> >>>
> >>> //System.out.println(""+ connection.getOutputStream());
> >>>
> >>> //System.out.println("After dataoutputstream..Line No-65");
> >>>
> >>> //System.out.println("Response Code="+ connection.getResponseCode);
> >>>
> >>> OutputStreamWriter dosout = new
> >>> OutputStreamWriter(connection.getOutputStream());
> >>> //System.out.println("After dosout object..Line No-63");
> >>> //dosout.write(str);
> >>> dosout.close ();
> >>>
> >>> BufferedReader in = new BufferedReader( new InputStreamReader(
> >>> connection.getInputStream()));
> >>>
> >>> String decodedString;
> >>> String tempstr = "";
> >>>
> >>>
> >>> while ((decodedString = in.readLine()) != null)
> >>> {
> >>> tempstr = tempstr + decodedString;
> >>> //out.println(decodedString);
> >>> }
> >>> out.println(tempstr);
> >>> in.close();
> >>> }
> >>> catch(Exception ex)
> >>> {
> >>> out.println("Exception->"+ex);
> >>> PrintWriter pw = response.getWriter();
> >>> ex.printStackTrace(pw);
> >>> }
> >>>
> >>>
> >>> %>
> >>>
> >>> Thanks in advance..
> >>>
> >>> Regards,
> >>> JItesh Dundas
> >>>
> >>> _______________________________________________
> >>> Biojava-l mailing list - Biojava-l@...
> >>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>
> >>
> > <ImportFromPubmed3.jsp>_______________________________________________
> > Biojava-l mailing list - Biojava-l@...
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland@...
> http://www.eaglegenomics.com/
>
>

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland@...
http://www.eaglegenomics.com/

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Fwd: Java Error:- XML Parsing Error: XML or text declaration not at start of entity

2009-11-24T06:48:55Z

Dear Sir/Madam,

FYI..
Jus trying to contribute to this mailing list and help.

Regards,
Jitesh Dundas

---------- Forwarded message ----------
From: jitesh dundas <jbdundas@...>
Date: Nov 24, 2009 8:17 PM
Subject: Re: [Biojava-l] Java Error:- XML Parsing Error: XML or text
declaration not at start of entity
To: Richard Holland <holland@...>

Dear Sir,

Thank you for your reply. I figured this problem out by sending records in
small sets. e.g. 20 pages per page.

It is like a pagination functionality. For each new page, we need to hit the
URl..

My functionality is working fine.I will be happy to share my code with you
(and anyone) who needs it.

I simply fetch data from the URL and write to an XML file. Next I just read
the XML file and show them in the web page to the user.

Again, I need to know how to fetch records for protein database. Two types
of searches are needed I suspect.

First we use the Esearch utility and then the Efetch utility to get the data
of the specific protein..

I welcome any suggestions on this !

Thank you everyone for your help.

Regards,
Jitesh Dundas

On 11/24/09, Richard Holland <holland@...> wrote:

>
> Your program takes an input 'txtURLString' - could you give an example of
> the value that this usually contains? I suspect that this URL is where your
> problem lies but without seeing an example value I couldn't say for sure.
>
> thanks,
> Richard
>
> On 8 Nov 2009, at 10:22, jitesh dundas wrote:
>
> > Dear Sir,
> >
> > My program is working fine and can send me an xml file with 20
> > records. However, it does not allow me to send large amounts of
> > records.
> >
> > For e.g. if I enter "cancer" it will return only 20 records.
> >
> > Can you please tell me what I should do next to get all those records.
> > Thank you in advance
> >
> > Regards,
> > Jitesh Dundas
> >
> > On Sun, Nov 1, 2009 at 9:36 PM, Andreas Prlic <andreas@...> wrote:
> >>
> >> Hi Jitesh,
> >>
> >> It is hard to read your code with all the formatting off probably due to
> email and many commented lines that don;t seem to get used. Can you provide
> the stacktrace, so we can see what part of biojava is affected?
> >>
> >> Probably a good strategy to write and debug this is to simply the
> problem into smaller steps. Try to first download the files you want to
> parse and write the code to parse them from the local file. That will avoid
> any issues you might encounter with networking and server/client
> communication. Once the parsing is working you could take it to the next
> step and add the server communication...
> >>
> >> Andreas
> >>
> >>
> >>
> >>
> >> On Sun, Nov 1, 2009 at 7:41 AM, jitesh dundas <jbdundas@...>
> wrote:
> >>>
> >>> Hi friends,
> >>>
> >>> I am getting this error on doing a post(using the code below) to this
> url->
> >>>
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer&reldate=10
> >>>
> >>> I have written this code in .jsp file. Later I will change it into
> servlet.
> >>>
> >>> Error:-
> >>> XML Parsing Error: XML or text declaration not at start of entity
> >>> Location:
> >>>
> http://localhost:8080/ProteomDb/ImportFromPubmed2.jsp?txtDbName=pubmed&txtTerm=cancer&txtreldate=10&comSDay=01&comSMonth=01&txtSYear=&comEDay=01&comEMonth=01&txtEYear=&txtURLString=http%3A%2F%2Feutils.ncbi.nlm.nih.gov%2Fentrez%2Feutils%2Fesearch.fcgi%3Fdb%3Dpubmed%26term%3Dcancer%26reldate%3D10&txtsubmit=Fetch+Data+From+NCBI
> >>> Line Number 11, Column 1:<?xml version="1.0" ?><!DOCTYPE eSearchResult
> >>> PUBLIC "-//NLM//DTD eSearchResult, 11 May 2002//EN" "
> >>> http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd
> "><eSearchResult><Count>2034</Count><RetMax>20</RetMax><RetStart>0</RetStart><IdList>
> >>> <Id>19877350</Id> <Id>19877304</Id> <Id>19877297</Id>
> >>> <Id>19877284</Id> <Id>19877271</Id> <Id>19877265</Id>
> >>> <Id>19877250</Id> <Id>19877245</Id> <Id>19877226</Id>
> >>> <Id>19877210</Id> <Id>19877179</Id> <Id>19877175</Id>
> >>> <Id>19877161</Id> <Id>19877159</Id> <Id>19877158</Id>
> >>> <Id>19877123</Id> <Id>19877122</Id> <Id>19877120</Id>
> >>> <Id>19877119</Id> <Id>19877118</Id>
> >>> </IdList><TranslationSet><Translation> <From>cancer</From>
> >>> <To>"neoplasms"[MeSH Terms] OR "neoplasms"[All Fields] OR "cancer"[All
> >>> Fields]</To> </Translation></TranslationSet><TranslationStack>
> >>> <TermSet> <Term>"neoplasms"[MeSH Terms]</Term> <Field>MeSH
> >>> Terms</Field> <Count>2082133</Count> <Explode>Y</Explode>
> >>> </TermSet> <TermSet> <Term>"neoplasms"[All
> Fields]</Term> <Field>All
> >>> Fields</Field> <Count>1634731</Count> <Explode>Y</Explode>
> >>> </TermSet> <OP>OR</OP> <TermSet> <Term>"cancer"[All
> Fields]</Term>
> >>> <Field>All
> Fields</Field> <Count>902537</Count> <Explode>Y</Explode>
> >>> </TermSet> <OP>OR</OP> <OP>GROUP</OP> <TermSet>
> >>>
> <Term>2009/10/22[EDAT]</Term> <Field>EDAT</Field> <Count>0</Count>
> >>> <Explode>Y</Explode> </TermSet> <TermSet>
> >>>
> <Term>2009/11/01[EDAT]</Term> <Field>EDAT</Field> <Count>0</Count>
> >>> <Explode>Y</Explode> </TermSet> <OP>RANGE</OP> <OP>AND</OP>
> >>> </TranslationStack><QueryTranslation>("neoplasms"[MeSH Terms] OR
> >>> "neoplasms"[All Fields] OR "cancer"[All Fields]) AND 2009/10/22[EDAT] :
> >>> 2009/11/01[EDAT]</QueryTranslation></eSearchResult>
> >>> ^
> >>>
> >>> As you can see, the XML output is coming fine but the above error does
> not
> >>> go..The output via this program should be just like hitting manually
> the
> >>> above URL in the browser..
> >>> The browser is Mozilla Firefox.
> >>>
> >>> Code:-
> >>>
> >>> <%@ page language = "java" %>
> >>> <%@ page import = "java.sql.*" %>
> >>> <%@ page import = "java.util.*" %>
> >>> <%@ page import = "java.io.*" %>
> >>> <%@ page import="java.lang.*" %>
> >>> <%@ page import="java.net.*" %>
> >>> <%@ page import="java.nio.*" %>
> >>> <%@ page contentType="text/xml; charset=utf-8" pageEncoding="UTF-8" %>
> >>>
> >>>
> >>> <%
> >>>
> >>> try
> >>> {
> >>> //String str = "<?xml version='1.0' ?>";
> >>> //out.println("<?xml version='1.0' encoding='utf-8' ?>");
> >>>
> >>> Properties systemSettings = System.getProperties();
> >>> systemSettings.put("http.proxyHost", "********");
> >>> systemSettings.put("http.proxyPort", "******");
> >>> systemSettings.put("sun.net.client.defaultConnectTimeout", "10000");
> >>> systemSettings.put("sun.net.client.defaultReadTimeout", "10000");
> >>>
> >>> //out.println("Properties Set");
> >>> Authenticator.setDefault(new Authenticator()
> >>> {
> >>> protected PasswordAuthentication getPasswordAuthentication()
> >>> {
> >>> return new PasswordAuthentication("**",
> >>> "******".toCharArray()); // specify ur user name password of iitb login
> >>> }
> >>> });
> >>>
> >>>
> >>> System.setProperties(systemSettings);
> >>> //out.println("After Authentication & Properties Settings");
> >>>
> >>> //create xml file.
> >>> //the input to google api
> >>> //String textAreaContent = request.getParameter("text");
> >>> String textAreaContent = "This si a tst";
> >>>
> >>> String str = "<?xml version='1.0' encoding='utf-8' ?>";
> >>>
> >>> //xml file generation ends here..
> >>> //FetchDataFromNCBI_URLString.jsp
> >>> String URLString = request.getParameter("txtURLString").trim();
> >>>
> >>> //URL url = new URL("
> >>>
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=protein&term=BAA20519
> >>> ");
> >>> URL url = new URL(URLString); //url string taken from user input.
> >>> HttpURLConnection connection = null;
> >>>
> >>> connection = (HttpURLConnection) url.openConnection();
> >>> System.out.println("After open connection");
> >>> connection.setRequestMethod("POST");
> >>> connection.setDoInput(true);
> >>> connection.setDoOutput(true);
> >>>
> >>> connection.setUseCaches(false);
> >>> connection.setAllowUserInteraction(false);
> >>> //connection.setFollowRedirects(true);
> >>> //connection.setInstanceFollowRedirects(true);
> >>> //System.out.println("Before-------------------");
> >>> connection.setRequestProperty ("Content-Type","text/xml;
> >>> charset=\"utf-8\"");
> >>> //System.out.println("After-------------------");
> >>>
> >>> //System.out.println(""+ connection.getOutputStream());
> >>>
> >>> //System.out.println("After dataoutputstream..Line No-65");
> >>>
> >>> //System.out.println("Response Code="+ connection.getResponseCode);
> >>>
> >>> OutputStreamWriter dosout = new
> >>> OutputStreamWriter(connection.getOutputStream());
> >>> //System.out.println("After dosout object..Line No-63");
> >>> //dosout.write(str);
> >>> dosout.close ();
> >>>
> >>> BufferedReader in = new BufferedReader( new InputStreamReader(
> >>> connection.getInputStream()));
> >>>
> >>> String decodedString;
> >>> String tempstr = "";
> >>>
> >>>
> >>> while ((decodedString = in.readLine()) != null)
> >>> {
> >>> tempstr = tempstr + decodedString;
> >>> //out.println(decodedString);
> >>> }
> >>> out.println(tempstr);
> >>> in.close();
> >>> }
> >>> catch(Exception ex)
> >>> {
> >>> out.println("Exception->"+ex);
> >>> PrintWriter pw = response.getWriter();
> >>> ex.printStackTrace(pw);
> >>> }
> >>>
> >>>
> >>> %>
> >>>
> >>> Thanks in advance..
> >>>
> >>> Regards,
> >>> JItesh Dundas
> >>>
> >>> _______________________________________________
> >>> Biojava-l mailing list - Biojava-l@...
> >>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>
> >>
> > <ImportFromPubmed3.jsp>_______________________________________________
> > Biojava-l mailing list - Biojava-l@...
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland@...
> http://www.eaglegenomics.com/
>
>

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Re: sequencing data analysis

2009-11-24T02:33:43Z

There's loads of things you can do. A good starting point is here:

http://biojava.org/wiki/BioJava:CookBook

cheers,
Richard

On 24 Nov 2009, at 10:14, <rabee.a.aa@...> <rabee.a.aa@...> wrote:

> Dear Biojava members,
> I'm new to Biojava and i would like to use it for analysis of next generation sequencing data.
> May i ask you about the available packages for analysis of sequencing data?
>
> Best Regards,
> Rabe
> _______________________________________________
> Biojava-l mailing list - Biojava-l@...
> http://lists.open-bio.org/mailman/listinfo/biojava-l

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland@...
http://www.eaglegenomics.com/

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sequencing data analysis

2009-11-24T02:14:30Z

Dear Biojava members,
I'm new to Biojava and i would like to use it for analysis of next generation sequencing data.
May i ask you about the available packages for analysis of sequencing data?

Best Regards,
Rabe
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Re: Java Error:- XML Parsing Error: XML or text declaration not at start of entity

2009-11-23T11:08:11Z

Your program takes an input 'txtURLString' - could you give an example of the value that this usually contains? I suspect that this URL is where your problem lies but without seeing an example value I couldn't say for sure.

thanks,
Richard

On 8 Nov 2009, at 10:22, jitesh dundas wrote:

> Dear Sir,
>
> My program is working fine and can send me an xml file with 20
> records. However, it does not allow me to send large amounts of
> records.
>
> For e.g. if I enter "cancer" it will return only 20 records.
>
> Can you please tell me what I should do next to get all those records.
> Thank you in advance
>
> Regards,
> Jitesh Dundas
>
> On Sun, Nov 1, 2009 at 9:36 PM, Andreas Prlic <andreas@...> wrote:
>>
>> Hi Jitesh,
>>
>> It is hard to read your code with all the formatting off probably due to email and many commented lines that don;t seem to get used. Can you provide the stacktrace, so we can see what part of biojava is affected?
>>
>> Probably a good strategy to write and debug this is to simply the problem into smaller steps. Try to first download the files you want to parse and write the code to parse them from the local file. That will avoid any issues you might encounter with networking and server/client communication. Once the parsing is working you could take it to the next step and add the server communication...
>>
>> Andreas
>>
>>
>>
>>
>> On Sun, Nov 1, 2009 at 7:41 AM, jitesh dundas <jbdundas@...> wrote:
>>>
>>> Hi friends,
>>>
>>> I am getting this error on doing a post(using the code below) to this url->
>>> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer&reldate=10
>>>
>>> I have written this code in .jsp file. Later I will change it into servlet.
>>>
>>> Error:-
>>> XML Parsing Error: XML or text declaration not at start of entity
>>> Location:
>>> http://localhost:8080/ProteomDb/ImportFromPubmed2.jsp?txtDbName=pubmed&txtTerm=cancer&txtreldate=10&comSDay=01&comSMonth=01&txtSYear=&comEDay=01&comEMonth=01&txtEYear=&txtURLString=http%3A%2F%2Feutils.ncbi.nlm.nih.gov%2Fentrez%2Feutils%2Fesearch.fcgi%3Fdb%3Dpubmed%26term%3Dcancer%26reldate%3D10&txtsubmit=Fetch+Data+From+NCBI
>>> Line Number 11, Column 1:<?xml version="1.0" ?><!DOCTYPE eSearchResult
>>> PUBLIC "-//NLM//DTD eSearchResult, 11 May 2002//EN" "
>>> http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd"><eSearchResult><Count>2034</Count><RetMax>20</RetMax><RetStart>0</RetStart><IdList>
>>> <Id>19877350</Id> <Id>19877304</Id> <Id>19877297</Id>
>>> <Id>19877284</Id> <Id>19877271</Id> <Id>19877265</Id>
>>> <Id>19877250</Id> <Id>19877245</Id> <Id>19877226</Id>
>>> <Id>19877210</Id> <Id>19877179</Id> <Id>19877175</Id>
>>> <Id>19877161</Id> <Id>19877159</Id> <Id>19877158</Id>
>>> <Id>19877123</Id> <Id>19877122</Id> <Id>19877120</Id>
>>> <Id>19877119</Id> <Id>19877118</Id>
>>> </IdList><TranslationSet><Translation> <From>cancer</From>
>>> <To>"neoplasms"[MeSH Terms] OR "neoplasms"[All Fields] OR "cancer"[All
>>> Fields]</To> </Translation></TranslationSet><TranslationStack>
>>> <TermSet> <Term>"neoplasms"[MeSH Terms]</Term> <Field>MeSH
>>> Terms</Field> <Count>2082133</Count> <Explode>Y</Explode>
>>> </TermSet> <TermSet> <Term>"neoplasms"[All Fields]</Term> <Field>All
>>> Fields</Field> <Count>1634731</Count> <Explode>Y</Explode>
>>> </TermSet> <OP>OR</OP> <TermSet> <Term>"cancer"[All Fields]</Term>
>>> <Field>All Fields</Field> <Count>902537</Count> <Explode>Y</Explode>
>>> </TermSet> <OP>OR</OP> <OP>GROUP</OP> <TermSet>
>>> <Term>2009/10/22[EDAT]</Term> <Field>EDAT</Field> <Count>0</Count>
>>> <Explode>Y</Explode> </TermSet> <TermSet>
>>> <Term>2009/11/01[EDAT]</Term> <Field>EDAT</Field> <Count>0</Count>
>>> <Explode>Y</Explode> </TermSet> <OP>RANGE</OP> <OP>AND</OP>
>>> </TranslationStack><QueryTranslation>("neoplasms"[MeSH Terms] OR
>>> "neoplasms"[All Fields] OR "cancer"[All Fields]) AND 2009/10/22[EDAT] :
>>> 2009/11/01[EDAT]</QueryTranslation></eSearchResult>
>>> ^
>>>
>>> As you can see, the XML output is coming fine but the above error does not
>>> go..The output via this program should be just like hitting manually the
>>> above URL in the browser..
>>> The browser is Mozilla Firefox.
>>>
>>> Code:-
>>>
>>> <%@ page language = "java" %>
>>> <%@ page import = "java.sql.*" %>
>>> <%@ page import = "java.util.*" %>
>>> <%@ page import = "java.io.*" %>
>>> <%@ page import="java.lang.*" %>
>>> <%@ page import="java.net.*" %>
>>> <%@ page import="java.nio.*" %>
>>> <%@ page contentType="text/xml; charset=utf-8" pageEncoding="UTF-8" %>
>>>
>>>
>>> <%
>>>
>>> try
>>> {
>>> //String str = "<?xml version='1.0' ?>";
>>> //out.println("<?xml version='1.0' encoding='utf-8' ?>");
>>>
>>> Properties systemSettings = System.getProperties();
>>> systemSettings.put("http.proxyHost", "********");
>>> systemSettings.put("http.proxyPort", "******");
>>> systemSettings.put("sun.net.client.defaultConnectTimeout", "10000");
>>> systemSettings.put("sun.net.client.defaultReadTimeout", "10000");
>>>
>>> //out.println("Properties Set");
>>> Authenticator.setDefault(new Authenticator()
>>> {
>>> protected PasswordAuthentication getPasswordAuthentication()
>>> {
>>> return new PasswordAuthentication("**",
>>> "******".toCharArray()); // specify ur user name password of iitb login
>>> }
>>> });
>>>
>>>
>>> System.setProperties(systemSettings);
>>> //out.println("After Authentication & Properties Settings");
>>>
>>> //create xml file.
>>> //the input to google api
>>> //String textAreaContent = request.getParameter("text");
>>> String textAreaContent = "This si a tst";
>>>
>>> String str = "<?xml version='1.0' encoding='utf-8' ?>";
>>>
>>> //xml file generation ends here..
>>> //FetchDataFromNCBI_URLString.jsp
>>> String URLString = request.getParameter("txtURLString").trim();
>>>
>>> //URL url = new URL("
>>> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=protein&term=BAA20519
>>> ");
>>> URL url = new URL(URLString); //url string taken from user input.
>>> HttpURLConnection connection = null;
>>>
>>> connection = (HttpURLConnection) url.openConnection();
>>> System.out.println("After open connection");
>>> connection.setRequestMethod("POST");
>>> connection.setDoInput(true);
>>> connection.setDoOutput(true);
>>>
>>> connection.setUseCaches(false);
>>> connection.setAllowUserInteraction(false);
>>> //connection.setFollowRedirects(true);
>>> //connection.setInstanceFollowRedirects(true);
>>> //System.out.println("Before-------------------");
>>> connection.setRequestProperty ("Content-Type","text/xml;
>>> charset=\"utf-8\"");
>>> //System.out.println("After-------------------");
>>>
>>> //System.out.println(""+ connection.getOutputStream());
>>>
>>> //System.out.println("After dataoutputstream..Line No-65");
>>>
>>> //System.out.println("Response Code="+ connection.getResponseCode);
>>>
>>> OutputStreamWriter dosout = new
>>> OutputStreamWriter(connection.getOutputStream());
>>> //System.out.println("After dosout object..Line No-63");
>>> //dosout.write(str);
>>> dosout.close ();
>>>
>>> BufferedReader in = new BufferedReader( new InputStreamReader(
>>> connection.getInputStream()));
>>>
>>> String decodedString;
>>> String tempstr = "";
>>>
>>>
>>> while ((decodedString = in.readLine()) != null)
>>> {
>>> tempstr = tempstr + decodedString;
>>> //out.println(decodedString);
>>> }
>>> out.println(tempstr);
>>> in.close();
>>> }
>>> catch(Exception ex)
>>> {
>>> out.println("Exception->"+ex);
>>> PrintWriter pw = response.getWriter();
>>> ex.printStackTrace(pw);
>>> }
>>>
>>>
>>> %>
>>>
>>> Thanks in advance..
>>>
>>> Regards,
>>> JItesh Dundas
>>>
>>> _______________________________________________
>>> Biojava-l mailing list - Biojava-l@...
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>
> <ImportFromPubmed3.jsp>_______________________________________________
> Biojava-l mailing list - Biojava-l@...
> http://lists.open-bio.org/mailman/listinfo/biojava-l

Re: Algorithm to compare protein sequences

2009-11-21T03:25:34Z

Hi,

if I get this one right you want to do three things.

1. create a multiple sequence alignment.

2. create a pairwise distance matrix from the alignment.

3. use a distance based tree construction method (Agglomerative clustering (UPGME, WPGMA..) or Neighbor Joining) to create a tree. The tree can be printed as newick string.

I don't know if all of this is possible with biojava. If not, I could at least provide code to create the pairwise distance matrix (including JC and Kimura corrections) and for the clustering algorithms. But I thought NJ and AgglomerativeClustering are already implemented, though I couldn't find the classes in the 1.7 API ?

If you don't need to do the computations programmatically, you can also try

http://bio.informatik.uni-jena.de/epos/

though with the currently released version you have to do the alignment externally. The next release will also provide a way to do multiple sequence alignments directly.

Another alternative is

http://gi.cebitec.uni-bielefeld.de/qalign

QAlign can be used to create the alignment (using clustalw, tcoffee or dialign) and create NJ or Agglomerative tree in one step. Nice thing is that you can manipulate the alignment (i.e. insert gaps) and the tree updated continuously

cheers,

thasso

On Nov 21, 2009, at 09:35 , Andreas Dräger wrote:

> Hi Mara,
>
> At the moment there are two alignment algorithms available:
> Smith-Waterman for local and Needleman-Wunsh for global alignment. In
> addition to that there is a package for hidden Markov models that is
> also able to perform sequence alignments (see the BioJava cookbook for
> examples). However, currently both approaches will write the alignment
> similar to the BLAST output and not in this Newick format (I am actually
> not familiar with that). I hope that helps.
>
> Cheers
> Andreas
>
> --
> Dipl.-Bioinform. Andreas Dräger
> Eberhard Karls University Tübingen
> Center for Bioinformatics (ZBIT)
> Sand 1
> 72076 Tübingen
> Germany
>
> Phone: +49-7071-29-70436
> Fax: +49-7071-29-5091
>
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@...
> http://lists.open-bio.org/mailman/listinfo/biojava-l

--
Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik
Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik
Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena
Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany

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Re: Algorithm to compare protein sequences

2009-11-21T00:35:19Z

Hi Mara,

At the moment there are two alignment algorithms available:
Smith-Waterman for local and Needleman-Wunsh for global alignment. In
addition to that there is a package for hidden Markov models that is
also able to perform sequence alignments (see the BioJava cookbook for
examples). However, currently both approaches will write the alignment
similar to the BLAST output and not in this Newick format (I am actually
not familiar with that). I hope that helps.

Cheers
Andreas

--
Dipl.-Bioinform. Andreas Dräger
Eberhard Karls University Tübingen
Center for Bioinformatics (ZBIT)
Sand 1
72076 Tübingen
Germany

Phone: +49-7071-29-70436
Fax: +49-7071-29-5091

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Algorithm to compare protein sequences

2009-11-20T21:43:52Z

Hello all,

I am looking for an algorithm to compare protein sequences and output the
result in Newick format, for a project. I was told that I could not use
UPGMA and Nearest Neighbor, algorithms. I'm new in working with phylogenetic
data. Any help is appreciated.

Thanks,
Mara
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Fwd: Newick parser

2009-11-17T11:57:50Z

Forwarding this to the users mailing list also, as there might be some
interest in the documentation.

---------- Forwarded message ----------
From: Tiago Antão <tiagoantao@...>
Date: 2009/11/17
Subject: Re: [Biojava-l] Newick parser
To: Richard Holland <holland@...>
Cc: Andreas Prlic <andreas@...>, biojava-dev
<biojava-dev@...>

As this was all fresh in my head, I wrote a small tutorial:

http://tiago.org/cc/2009/11/17/reading-newicknexus-phylogenetic-trees-with-biojava/

As I don't follow the biojava mailing list regularly (or bug reports),
if some bug arises on this code, feel free to send me an email to my
personal account: If I have some time to spare, I will have a look at
it.

Tiago

2009/11/17 Richard Holland <holland@...>:

> Sorry - forgot to change the filenames in the test (under the new modular system they're in a different place than in the non-modular codebase that Tiago was working from). Fixed and committed.
>
> On 17 Nov 2009, at 19:23, Andreas Prlic wrote:
>
>> Hi Richard,
>>
>> I just did an update of my checkout and it seems the -phylo unit tests
>> don't compile any more. Can you take a look?
>>
>> Thanks,
>> Andreas
>>
>> Test set: org.biojavax.bio.phylo.io.nexus.TreesBlockTest
>> -------------------------------------------------------------------------------
>> Tests run: 9, Failures: 0, Errors: 9, Skipped: 0, Time elapsed: 0.063
>> sec <<< FAILURE!
>> testSimple(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) Time
>> elapsed: 0.021 sec <<< ERROR!
>> java.lang.NullPointerException
>> at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160)
>> at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175)
>> at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139)
>> at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testSimple(TreesBlockTest.java:63)
>>
>> testThreeOffspring(org.biojavax.bio.phylo.io.nexus.TreesBlockTest)
>> Time elapsed: 0.002 sec <<< ERROR!
>> java.lang.NullPointerException
>> at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160)
>> at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175)
>> at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139)
>> at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testThreeOffspring(TreesBlockTest.java:70
>>
>> 2009/11/16 Richard Holland <holland@...>:
>>> Patch applied to the trunk of biojava-live. Thanks for fixing it!
>>>
>>> cheers,
>>> Richard
>>>
>>> On 15 Nov 2009, at 23:19, Tiago Antão wrote:
>>>
>>>> Hi,
>>>>
>>>> I have made the changes as discussed, the code is attached to the
>>>> bugzilla bug concerning part of the issues that were found.
>>>> A few notes:
>>>>
>>>> 1. There is a ParserException raised on TreeBlock. Tough there is a
>>>> TreeBlockParser, most of the important parsing was (and still is!)
>>>> being made on TreeBlock. I would imagine that this is not the best
>>>> design, but I did not change it.
>>>> 2. I made some test cases. Also included.
>>>> 3. I don't mind producing some documentation, in case you accept the code.
>>>> 4. I noticed a few minor bugs more (like eating spaces in the names of
>>>> nodes). But they are really minor.
>>>> 5. The API was changed, but I suppose not many people were parsing
>>>> trees. If there were people parsing trees most probably the bug on not
>>>> being able to process trees that are not binary would have been
>>>> detected as it is pretty major.
>>>>
>>>> Tiago
>>>>
>>>> --
>>>> “Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci
>>>>
>>>> _______________________________________________
>>>> Biojava-l mailing list - Biojava-l@...
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>> --
>>> Richard Holland, BSc MBCS
>>> Operations and Delivery Director, Eagle Genomics Ltd
>>> T: +44 (0)1223 654481 ext 3 | E: holland@...
>>> http://www.eaglegenomics.com/
>>>
>>>
>>> _______________________________________________
>>> Biojava-l mailing list - Biojava-l@...
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland@...
> http://www.eaglegenomics.com/
>
>

--
“Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci

--
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Re: Newick parser

2009-11-16T09:52:56Z

I've submitted a patch to 2679. Please have a look and see if you like it.

2009/11/16 Richard Holland <holland@...>:

> yes please!
>
> On 16 Nov 2009, at 12:35, Tiago Antão wrote:
>
>> I can just easily solve 2679, as it is precisely on the file that I
>> was changing. In case there is interest I'll just solve it.
>>
>> 2009/11/16 Richard Holland <holland@...>:
>>> Patch applied to the trunk of biojava-live. Thanks for fixing it!
>>>
>>> cheers,
>>> Richard
>>>
>>> On 15 Nov 2009, at 23:19, Tiago Antão wrote:
>>>
>>>> Hi,
>>>>
>>>> I have made the changes as discussed, the code is attached to the
>>>> bugzilla bug concerning part of the issues that were found.
>>>> A few notes:
>>>>
>>>> 1. There is a ParserException raised on TreeBlock. Tough there is a
>>>> TreeBlockParser, most of the important parsing was (and still is!)
>>>> being made on TreeBlock. I would imagine that this is not the best
>>>> design, but I did not change it.
>>>> 2. I made some test cases. Also included.
>>>> 3. I don't mind producing some documentation, in case you accept the code.
>>>> 4. I noticed a few minor bugs more (like eating spaces in the names of
>>>> nodes). But they are really minor.
>>>> 5. The API was changed, but I suppose not many people were parsing
>>>> trees. If there were people parsing trees most probably the bug on not
>>>> being able to process trees that are not binary would have been
>>>> detected as it is pretty major.
>>>>
>>>> Tiago
>>>>
>>>> --
>>>> “Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci
>>>>
>>>> _______________________________________________
>>>> Biojava-l mailing list - Biojava-l@...
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>> --
>>> Richard Holland, BSc MBCS
>>> Operations and Delivery Director, Eagle Genomics Ltd
>>> T: +44 (0)1223 654481 ext 3 | E: holland@...
>>> http://www.eaglegenomics.com/
>>>
>>>
>>
>>
>>
>> --
>> “Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland@...
> http://www.eaglegenomics.com/
>
>

--
“Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci

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Re: Newick parser

2009-11-16T04:41:50Z

yes please!

On 16 Nov 2009, at 12:35, Tiago Antão wrote:

> I can just easily solve 2679, as it is precisely on the file that I
> was changing. In case there is interest I'll just solve it.
>
> 2009/11/16 Richard Holland <holland@...>:
>> Patch applied to the trunk of biojava-live. Thanks for fixing it!
>>
>> cheers,
>> Richard
>>
>> On 15 Nov 2009, at 23:19, Tiago Antão wrote:
>>
>>> Hi,
>>>
>>> I have made the changes as discussed, the code is attached to the
>>> bugzilla bug concerning part of the issues that were found.
>>> A few notes:
>>>
>>> 1. There is a ParserException raised on TreeBlock. Tough there is a
>>> TreeBlockParser, most of the important parsing was (and still is!)
>>> being made on TreeBlock. I would imagine that this is not the best
>>> design, but I did not change it.
>>> 2. I made some test cases. Also included.
>>> 3. I don't mind producing some documentation, in case you accept the code.
>>> 4. I noticed a few minor bugs more (like eating spaces in the names of
>>> nodes). But they are really minor.
>>> 5. The API was changed, but I suppose not many people were parsing
>>> trees. If there were people parsing trees most probably the bug on not
>>> being able to process trees that are not binary would have been
>>> detected as it is pretty major.
>>>
>>> Tiago
>>>
>>> --
>>> “Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci
>>>
>>> _______________________________________________
>>> Biojava-l mailing list - Biojava-l@...
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>> --
>> Richard Holland, BSc MBCS
>> Operations and Delivery Director, Eagle Genomics Ltd
>> T: +44 (0)1223 654481 ext 3 | E: holland@...
>> http://www.eaglegenomics.com/
>>
>>
>
>
>
> --
> “Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci

Re: Newick parser

2009-11-16T04:35:11Z

I can just easily solve 2679, as it is precisely on the file that I
was changing. In case there is interest I'll just solve it.

2009/11/16 Richard Holland <holland@...>:

> Patch applied to the trunk of biojava-live. Thanks for fixing it!
>
> cheers,
> Richard
>
> On 15 Nov 2009, at 23:19, Tiago Antão wrote:
>
>> Hi,
>>
>> I have made the changes as discussed, the code is attached to the
>> bugzilla bug concerning part of the issues that were found.
>> A few notes:
>>
>> 1. There is a ParserException raised on TreeBlock. Tough there is a
>> TreeBlockParser, most of the important parsing was (and still is!)
>> being made on TreeBlock. I would imagine that this is not the best
>> design, but I did not change it.
>> 2. I made some test cases. Also included.
>> 3. I don't mind producing some documentation, in case you accept the code.
>> 4. I noticed a few minor bugs more (like eating spaces in the names of
>> nodes). But they are really minor.
>> 5. The API was changed, but I suppose not many people were parsing
>> trees. If there were people parsing trees most probably the bug on not
>> being able to process trees that are not binary would have been
>> detected as it is pretty major.
>>
>> Tiago
>>
>> --
>> “Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci
>>
>> _______________________________________________
>> Biojava-l mailing list - Biojava-l@...
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland@...
> http://www.eaglegenomics.com/
>
>

Re: Newick parser

2009-11-16T00:39:02Z

Patch applied to the trunk of biojava-live. Thanks for fixing it!

cheers,
Richard

On 15 Nov 2009, at 23:19, Tiago Antão wrote:

> Hi,
>
> I have made the changes as discussed, the code is attached to the
> bugzilla bug concerning part of the issues that were found.
> A few notes:
>
> 1. There is a ParserException raised on TreeBlock. Tough there is a
> TreeBlockParser, most of the important parsing was (and still is!)
> being made on TreeBlock. I would imagine that this is not the best
> design, but I did not change it.
> 2. I made some test cases. Also included.
> 3. I don't mind producing some documentation, in case you accept the code.
> 4. I noticed a few minor bugs more (like eating spaces in the names of
> nodes). But they are really minor.
> 5. The API was changed, but I suppose not many people were parsing
> trees. If there were people parsing trees most probably the bug on not
> being able to process trees that are not binary would have been
> detected as it is pretty major.
>
> Tiago
>
> --
> “Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l@...
> http://lists.open-bio.org/mailman/listinfo/biojava-l

Re: JMol I/O

2009-11-15T20:41:57Z

Hi Andy,

probably you are trying to visualize a small molecule in Jmol, but the
visualization script you are sending only works if you have several
C-alpha atoms available. Try something like "select * ; spacefill
on;". Jmol has a powerful scripting language which is probably worth
having a look at, if you want to work with it more closely.

Andreas

On Sun, Nov 15, 2009 at 2:07 PM, Andy Lu <andylu0320@...> wrote:

> Hi, sorry to bother everyone again.
> But I have a simple quesiton, I am using the SimpleJMolExample.java provided
> on the website and it works. But for a pdb file containing about 20 atoms,
> all of the atoms shows up on JMol for 1 second and then disappears, is it
> because the color changes or something or some atom size restriction? It
> works for files that contain much larger number of atoms.
> If I try to open a file manually from JMol through the open option, it shows
> up nicely. Is there a way that I can make the pdb file displayed on JMol
> through Biojava the same color/display as the one if I open it manually
> though JMol?
> Any help would be greatly appreciated!
> Thank you!
>
> --
> Andy Lu
> _______________________________________________
> Biojava-l mailing list - Biojava-l@...
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

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Newick parser

2009-11-15T15:19:46Z

Hi,

I have made the changes as discussed, the code is attached to the
bugzilla bug concerning part of the issues that were found.
A few notes:

1. There is a ParserException raised on TreeBlock. Tough there is a
TreeBlockParser, most of the important parsing was (and still is!)
being made on TreeBlock. I would imagine that this is not the best
design, but I did not change it.
2. I made some test cases. Also included.
3. I don't mind producing some documentation, in case you accept the code.
4. I noticed a few minor bugs more (like eating spaces in the names of
nodes). But they are really minor.
5. The API was changed, but I suppose not many people were parsing
trees. If there were people parsing trees most probably the bug on not
being able to process trees that are not binary would have been
detected as it is pretty major.

Tiago

--
“Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci

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JMol I/O

2009-11-15T14:07:41Z

Hi, sorry to bother everyone again.
But I have a simple quesiton, I am using the SimpleJMolExample.java provided
on the website and it works. But for a pdb file containing about 20 atoms,
all of the atoms shows up on JMol for 1 second and then disappears, is it
because the color changes or something or some atom size restriction? It
works for files that contain much larger number of atoms.
If I try to open a file manually from JMol through the open option, it shows
up nicely. Is there a way that I can make the pdb file displayed on JMol
through Biojava the same color/display as the one if I open it manually
though JMol?
Any help would be greatly appreciated!
Thank you!

--
Andy Lu
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Re: How do I read a FASTA file containing protein sequences in lowercase?

2009-11-13T07:04:27Z

I've applied the patch to the trunk of biojava-live. Thanks!

Richard

On 9 Nov 2009, at 16:26, Carl Mäsak wrote:

> Richard (>):
>> Ah OK I see what's going on.
>>
>> The convenience method you're using, RichSequence.IOTools.readStream(), uses
>> FastaFormat to try and guess the alphabet to use based on the first line of
>> the input sequence.
>>
>> In FastaFormat, it does this by searching for matching non-DNA symbols. The
>> search is case-sensitive:
>>
>> protected static final Pattern aminoAcids =
>> Pattern.compile(".*[FLIPQE].*");
>>
>> FastaFormat needs patching to make this pattern non-case-sensitive.
>
> Patch attached.
>
> I also took the opportunity to remove the occurrences of .* in the
> Pattern above. Generally, once should be using Matcher.find() when one
> is interested in matching a part of a string. This is more efficient
> than using Matcher.matches() and surrounding the desired regular
> expression with .*, since the latter will cause a lot of unnecessary
> backtracking and make the search quadratic.
>
> This effect only shows up for very long strings, but long strings can
> and do happen in bioinformatics. The below measurements show the
> quadratic behaviour of the former approach.
>
> $ for length in 100 1000 10000 100000 1000000; do (time java
> WithDotStar $length) 2>&1 | grep real; done
> real 0m0.371s
> real 0m0.367s
> real 0m0.577s
> real 0m2.735s
> real 0m25.275s
>
> $ for length in 100 1000 10000 100000 1000000; do (time java
> WithoutDotStar $length) 2>&1 | grep real; done
> real 0m0.309s
> real 0m0.361s
> real 0m0.468s
> real 0m1.184s
> real 0m9.703s
>
> Kindly,
> // Carl
> <aminoAcids.patch><WithDotStar.java><WithoutDotStar.java>

Re: Newick/Nexus processing of non-binary trees

2009-11-13T06:54:08Z

2009/11/13 Thasso Griebel <thasso.griebel@...>:
> just my two cents, but I would go with a default weight of 1.0. If you read
> something unweighted you would ignore the edge weights anyways, but, for
> example, if you write something simple that computes path lengths, a default
> weight of 1.0 ensures that the method also works for "unweighted" trees,
> where the length of a path is defined as the number of edges you need to
> traverse to move from say A to B. I think the argument also hold for other
> algorithms used on trees and graphs.

OK, I will do this.
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Re: Newick/Nexus processing of non-binary trees

2009-11-13T06:51:41Z

Hi,

> 1. A weighted version is enough. If branch lengths are not specified,
> then weights could be set to 0. There there would not be a decrease in
> functionality.

just my two cents, but I would go with a default weight of 1.0. If you
read something unweighted you would ignore the edge weights anyways,
but, for example, if you write something simple that computes path
lengths, a default weight of 1.0 ensures that the method also works
for "unweighted" trees, where the length of a path is defined as the
number of edges you need to traverse to move from say A to B. I think
the argument also hold for other algorithms used on trees and graphs.

anyways, just my two cent.

-thasso

--
Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik
Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik
Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena
Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany

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Re: Newick/Nexus processing of non-binary trees

2009-11-13T04:42:03Z

i'm all for that.

The original code was developed by a Google Summer of Code student, who we haven't heard much from since. :(

cheers,
Richard

On 13 Nov 2009, at 12:25, Tiago Antão wrote:

> Hi,
>
>> My suggestion: for somebody else to verify my findings. I might be
>> doing something stupidly wrong. Maybe things are correct. Just a
>> simple tree like (1,2,3) (as long as it is not binary) - should expose
>> the problem.
>>
>
> Has nobody answered here is my take:
>
> 1. The error reported probably exists
> 2. Most probably nobody is using the parser (as it only supports binary trees).
>
> In this light, changing the API should not be a problem at all.
>
> I would not mind correcting the problem (I have already corrected the
> previous 2 ones in my local version).
> I would suggest removing the call to the unweighted graph. Reasons:
> 1. A weighted version is enough. If branch lengths are not specified,
> then weights could be set to 0. There there would not be a decrease in
> functionality.
> 2. Severely reducing the size of the code is important. Clearly the
> code is not much maintained (and I am not offering to maintain it in
> the long run, just putting it in good shape) and not much used.
> Therefore a smaller, more easy to manage code base makes even more
> sense.
>
> If you accept a solution along these lines. I would correct all the
> bugs and also include test code (which is also missing).
>
>
>
> --
> "The hottest places in hell are reserved for those who, in times of
> moral crisis, maintain a neutrality." - Dante

Re: Newick/Nexus processing of non-binary trees

2009-11-13T04:25:41Z

Hi,

> My suggestion: for somebody else to verify my findings. I might be
> doing something stupidly wrong. Maybe things are correct. Just a
> simple tree like (1,2,3) (as long as it is not binary) - should expose
> the problem.
>

Has nobody answered here is my take:

1. The error reported probably exists
2. Most probably nobody is using the parser (as it only supports binary trees).

In this light, changing the API should not be a problem at all.

I would not mind correcting the problem (I have already corrected the
previous 2 ones in my local version).
I would suggest removing the call to the unweighted graph. Reasons:
1. A weighted version is enough. If branch lengths are not specified,
then weights could be set to 0. There there would not be a decrease in
functionality.
2. Severely reducing the size of the code is important. Clearly the
code is not much maintained (and I am not offering to maintain it in
the long run, just putting it in good shape) and not much used.
Therefore a smaller, more easy to manage code base makes even more
sense.

If you accept a solution along these lines. I would correct all the
bugs and also include test code (which is also missing).

--
"The hottest places in hell are reserved for those who, in times of
moral crisis, maintain a neutrality." - Dante
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Re: SeqIOTools deprecated, looking for alternatives // RichSeq.IOTools

2009-11-13T03:21:47Z

Hello,

The file you are parsing is not a valid EMBL format file. The EMBL format is specified here:

http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_4

and this is what the file should look like for your accession:

http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&id=AJ243265&Submit=Go

The most obvious problems in your file are the absence of the required 'XX' section delimiters, and an invalid ID line. There might be other problems too but I haven't checked the whole file, just the first few lines.

The deprecated SeqIOTools really didn't care if the file was valid or not, they basically just made a copy of all the lines in an internal token/value map. They made no attempt to parse or understand the data in each line. The new RichSequence-based parsers actually attempt to enforce the file format definitions and break down and understand the contents of each line. This means that they will reject any file that does not strictly conform to the specified format.

cheers,
Richard

On 12 Nov 2009, at 13:18, Oliver Stolpe wrote:

> Hello *,
>
> the cookbook uses in its examples the SeqIOTools-class for reading the files. But in the API it is marked as deprecated. Now I am looking for alternatives, so I searched the list and internet and found out that biojavax provides methods and classes for reading the files (RichSequence.IOTools).
>
> For example, I try to read an EMBL-file:
>
> --begin:code--
>
> BufferedReader br = new BufferedReader(new FileReader(filename));
> Namespace ns = RichObjectFactory.getDefaultNamespace();
> RichSequenceIterator seqs = RichSequence.IOTools.readEMBLDNA(br, ns);
>
> while (seqs.hasNext()) {
> RichSequence seq = seqs.nextRichSequence();
> System.out.println(seq.getName() + ":" + seq.getAnnotation().asMap());
> }
>
> --end:code--
>
> But I always get this error message:
>
> --begin:error--
>
> org.biojava.bio.BioException: Could not read sequence
> at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
> at ReadGenbankFile.EMBL(ReadGenbankFile.java:42)
> at ReadGenbankFile.main(ReadGenbankFile.java:85)
> Caused by: org.biojava.bio.seq.io.ParseException:
>
> A Exception Has Occurred During Parsing.
> Please submit the details that follow to biojava-l@... or post a bug report to http://bugzilla.open-bio.org/
>
> Format_object=org.biojavax.bio.seq.io.EMBLFormat
> Accession=null
> Id=not set
> Comments=
> Parse_block=ID AJ243265_2; parent: AJ243265AC AJ243265;FT CDS join(<1082..1272,2484..2638,4926..>5041)
> /codon_start=3
> /gene="PGM1"
> /product="phosphoglucomutase 1"
> /function="carbohydrate metabolism"
> /EC_number="5.4.2.2"
> /db_xref="GOA:Q9H1D2"
> /db_xref="HGNC:8905"
> /db_xref="HSSP:3PMG"
> /db_xref="InterPro:IPR016055"
> /db_xref="UniProtKB/TrEMBL:Q9H1D2"
> /protein_id="CAC19809.1"
> /translation="VGPYVKKILCEELGAPANSAVNCVPLEDFGGHHPDPNLTYAADLV
> ETMKSGEHDFGAAFDGDGDRNMILGKHGFFVNPSDSVAVIAANTFSIPYFQQTGVRGFA
> RSMPTSGALDRVASATKIALYETPTGWKFFGNLMDASKLSLCGEESFGT"SQ Sequence 462 BP;
> Stack trace follows ....
>
>
> at org.biojavax.bio.seq.io.EMBLFormat.readSection(EMBLFormat.java:775)
> at org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:284)
> at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
> ... 2 more
> Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: -3
> at java.lang.String.substring(String.java:1949)
> at java.lang.String.substring(String.java:1916)
> at org.biojavax.bio.seq.io.EMBLFormat.readSection(EMBLFormat.java:761)
> ... 4 more
>
> --end:error--
>
> The file looks all ok I think and works well with the deprecated SeqIOTools:
>
> --begin:embl-file--
> ID AJ243265_2; parent: AJ243265
> AC AJ243265;
> FT CDS join(<1082..1272,2484..2638,4926..>5041)
> FT /codon_start=3
> FT /gene="PGM1"
> FT /product="phosphoglucomutase 1"
> FT /function="carbohydrate metabolism"
> FT /EC_number="5.4.2.2"
> FT /db_xref="GOA:Q9H1D2"
> FT /db_xref="HGNC:8905"
> FT /db_xref="HSSP:3PMG"
> FT /db_xref="InterPro:IPR016055"
> FT /db_xref="UniProtKB/TrEMBL:Q9H1D2"
> FT /protein_id="CAC19809.1"
> FT /translation="VGPYVKKILCEELGAPANSAVNCVPLEDFGGHHPDPNLTYAADLV
> FT ETMKSGEHDFGAAFDGDGDRNMILGKHGFFVNPSDSVAVIAANTFSIPYFQQTGVRGFA
> FT RSMPTSGALDRVASATKIALYETPTGWKFFGNLMDASKLSLCGEESFGT"
> SQ Sequence 462 BP;
> ttgtgggacc gtatgtaaag aagatcctct gtgaagaact cggtgcccct gcgaactcgg 60
> cagttaactg cgttcctctg gaggactttg gaggccacca ccctgacccc aacctcacct 120
> atgcagctga cctggtggag accatgaagt caggagagca tgattttggg gctgcctttg 180
> atggagatgg ggatcgaaac atgattctgg gcaagcatgg gttctttgtg aacccttcag 240
> actctgtggc tgtcattgct gccaacacct tcagcattcc gtatttccag cagactgggg 300
> tccgcggttt tgcacggagc atgcccacga gtggtgctct ggaccgggtg gctagtgcta 360
> caaagattgc tttgtatgag accccaactg gctggaagtt ttttgggaat ttgatggacg 420
> cgagcaaact gtccctttgt ggggaggaga gcttcgggac cg 462
> //
> --end:embl-file--
>
> The parser always crashes before reading the sequence (ttgt..., directly after the BP;).
>
> Any suggestions how I get this work?
> Or are there other alternatives for substituting the deprecated SeqIOTools-class?
>
> Thanks in advance,
>
> with best regards,
>
> Oliver
> _______________________________________________
> Biojava-l mailing list - Biojava-l@...
> http://lists.open-bio.org/mailman/listinfo/biojava-l

SeqIOTools deprecated, looking for alternatives // RichSeq.IOTools

2009-11-12T05:18:52Z

Hello *,

the cookbook uses in its examples the SeqIOTools-class for reading the
files. But in the API it is marked as deprecated. Now I am looking for
alternatives, so I searched the list and internet and found out that
biojavax provides methods and classes for reading the files
(RichSequence.IOTools).

For example, I try to read an EMBL-file:

--begin:code--

BufferedReader br = new BufferedReader(new FileReader(filename));
Namespace ns = RichObjectFactory.getDefaultNamespace();
RichSequenceIterator seqs = RichSequence.IOTools.readEMBLDNA(br, ns);

while (seqs.hasNext()) {
RichSequence seq = seqs.nextRichSequence();
System.out.println(seq.getName() + ":" + seq.getAnnotation().asMap());
}

--end:code--

But I always get this error message:

--begin:error--

org.biojava.bio.BioException: Could not read sequence
at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
at ReadGenbankFile.EMBL(ReadGenbankFile.java:42)
at ReadGenbankFile.main(ReadGenbankFile.java:85)
Caused by: org.biojava.bio.seq.io.ParseException:

A Exception Has Occurred During Parsing.
Please submit the details that follow to biojava-l@... or post a
bug report to http://bugzilla.open-bio.org/

Format_object=org.biojavax.bio.seq.io.EMBLFormat
Accession=null
Id=not set
Comments=
Parse_block=ID AJ243265_2; parent: AJ243265AC AJ243265;FT
CDS join(<1082..1272,2484..2638,4926..>5041)
/codon_start=3
/gene="PGM1"
/product="phosphoglucomutase 1"
/function="carbohydrate metabolism"
/EC_number="5.4.2.2"
/db_xref="GOA:Q9H1D2"
/db_xref="HGNC:8905"
/db_xref="HSSP:3PMG"
/db_xref="InterPro:IPR016055"
/db_xref="UniProtKB/TrEMBL:Q9H1D2"
/protein_id="CAC19809.1"
/translation="VGPYVKKILCEELGAPANSAVNCVPLEDFGGHHPDPNLTYAADLV
ETMKSGEHDFGAAFDGDGDRNMILGKHGFFVNPSDSVAVIAANTFSIPYFQQTGVRGFA
RSMPTSGALDRVASATKIALYETPTGWKFFGNLMDASKLSLCGEESFGT"SQ
Sequence 462 BP;
Stack trace follows ....

at
org.biojavax.bio.seq.io.EMBLFormat.readSection(EMBLFormat.java:775)
at
org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:284)
at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
... 2 more
Caused by: java.lang.StringIndexOutOfBoundsException: String index out
of range: -3
at java.lang.String.substring(String.java:1949)
at java.lang.String.substring(String.java:1916)
at
org.biojavax.bio.seq.io.EMBLFormat.readSection(EMBLFormat.java:761)
... 4 more

--end:error--

The file looks all ok I think and works well with the deprecated SeqIOTools:

--begin:embl-file--
ID AJ243265_2; parent: AJ243265
AC AJ243265;
FT CDS join(<1082..1272,2484..2638,4926..>5041)
FT /codon_start=3
FT /gene="PGM1"
FT /product="phosphoglucomutase 1"
FT /function="carbohydrate metabolism"
FT /EC_number="5.4.2.2"
FT /db_xref="GOA:Q9H1D2"
FT /db_xref="HGNC:8905"
FT /db_xref="HSSP:3PMG"
FT /db_xref="InterPro:IPR016055"
FT /db_xref="UniProtKB/TrEMBL:Q9H1D2"
FT /protein_id="CAC19809.1"
FT
/translation="VGPYVKKILCEELGAPANSAVNCVPLEDFGGHHPDPNLTYAADLV
FT
ETMKSGEHDFGAAFDGDGDRNMILGKHGFFVNPSDSVAVIAANTFSIPYFQQTGVRGFA
FT RSMPTSGALDRVASATKIALYETPTGWKFFGNLMDASKLSLCGEESFGT"
SQ Sequence 462 BP;
ttgtgggacc gtatgtaaag aagatcctct gtgaagaact cggtgcccct
gcgaactcgg 60
cagttaactg cgttcctctg gaggactttg gaggccacca ccctgacccc
aacctcacct 120
atgcagctga cctggtggag accatgaagt caggagagca tgattttggg
gctgcctttg 180
atggagatgg ggatcgaaac atgattctgg gcaagcatgg gttctttgtg
aacccttcag 240
actctgtggc tgtcattgct gccaacacct tcagcattcc gtatttccag
cagactgggg 300
tccgcggttt tgcacggagc atgcccacga gtggtgctct ggaccgggtg
gctagtgcta 360
caaagattgc tttgtatgag accccaactg gctggaagtt ttttgggaat
ttgatggacg 420
cgagcaaact gtccctttgt ggggaggaga gcttcgggac
cg 462
//
--end:embl-file--

The parser always crashes before reading the sequence (ttgt..., directly
after the BP;).

Any suggestions how I get this work?
Or are there other alternatives for substituting the deprecated
SeqIOTools-class?

Thanks in advance,

with best regards,

Oliver
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Re: Java Error:- XML Parsing Error: XML or text declaration not at start of entity

2009-11-10T06:23:10Z

Dear Friends,

Thank you for your help and advise.

The code in the mentioned URL is working fine ->
http://gist.github.com/229248 (this is my code that has been uploaded by a
wise group member. Many thanks to him for doing that)

Hope this helps..

Regards,
JItesh Dundas

On Sun, Nov 8, 2009 at 3:52 PM, jitesh dundas <jbdundas@...> wrote:

> Dear Sir,
>
> My program is working fine and can send me an xml file with 20
> records. However, it does not allow me to send large amounts of
> records.
>
> For e.g. if I enter "cancer" it will return only 20 records.
>
> Can you please tell me what I should do next to get all those records.
> Thank you in advance
>
> Regards,
> Jitesh Dundas
>
> On Sun, Nov 1, 2009 at 9:36 PM, Andreas Prlic <andreas@...> wrote:
> >
> > Hi Jitesh,
> >
> > It is hard to read your code with all the formatting off probably due to
> email and many commented lines that don;t seem to get used. Can you provide
> the stacktrace, so we can see what part of biojava is affected?
> >
> > Probably a good strategy to write and debug this is to simply the problem
> into smaller steps. Try to first download the files you want to parse and
> write the code to parse them from the local file. That will avoid any
> issues you might encounter with networking and server/client communication.
> Once the parsing is working you could take it to the next step and add the
> server communication...
> >
> > Andreas
> >
> >
> >
> >
> > On Sun, Nov 1, 2009 at 7:41 AM, jitesh dundas <jbdundas@...>
> wrote:
> >>
> >> Hi friends,
> >>
> >> I am getting this error on doing a post(using the code below) to this
> url->
> >>
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer&reldate=10
> >>
> >> I have written this code in .jsp file. Later I will change it into
> servlet.
> >>
> >> Error:-
> >> XML Parsing Error: XML or text declaration not at start of entity
> >> Location:
> >>
> http://localhost:8080/ProteomDb/ImportFromPubmed2.jsp?txtDbName=pubmed&txtTerm=cancer&txtreldate=10&comSDay=01&comSMonth=01&txtSYear=&comEDay=01&comEMonth=01&txtEYear=&txtURLString=http%3A%2F%2Feutils.ncbi.nlm.nih.gov%2Fentrez%2Feutils%2Fesearch.fcgi%3Fdb%3Dpubmed%26term%3Dcancer%26reldate%3D10&txtsubmit=Fetch+Data+From+NCBI
> >> Line Number 11, Column 1:<?xml version="1.0" ?><!DOCTYPE eSearchResult
> >> PUBLIC "-//NLM//DTD eSearchResult, 11 May 2002//EN" "
> >> http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd
> "><eSearchResult><Count>2034</Count><RetMax>20</RetMax><RetStart>0</RetStart><IdList>
> >> <Id>19877350</Id> <Id>19877304</Id> <Id>19877297</Id>
> >> <Id>19877284</Id> <Id>19877271</Id> <Id>19877265</Id>
> >> <Id>19877250</Id> <Id>19877245</Id> <Id>19877226</Id>
> >> <Id>19877210</Id> <Id>19877179</Id> <Id>19877175</Id>
> >> <Id>19877161</Id> <Id>19877159</Id> <Id>19877158</Id>
> >> <Id>19877123</Id> <Id>19877122</Id> <Id>19877120</Id>
> >> <Id>19877119</Id> <Id>19877118</Id>
> >> </IdList><TranslationSet><Translation> <From>cancer</From>
> >> <To>"neoplasms"[MeSH Terms] OR "neoplasms"[All Fields] OR "cancer"[All
> >> Fields]</To> </Translation></TranslationSet><TranslationStack>
> >> <TermSet> <Term>"neoplasms"[MeSH Terms]</Term> <Field>MeSH
> >> Terms</Field> <Count>2082133</Count> <Explode>Y</Explode>
> >> </TermSet> <TermSet> <Term>"neoplasms"[All Fields]</Term>
> <Field>All
> >> Fields</Field> <Count>1634731</Count> <Explode>Y</Explode>
> >> </TermSet> <OP>OR</OP> <TermSet> <Term>"cancer"[All
> Fields]</Term>
> >> <Field>All Fields</Field> <Count>902537</Count>
> <Explode>Y</Explode>
> >> </TermSet> <OP>OR</OP> <OP>GROUP</OP> <TermSet>
> >> <Term>2009/10/22[EDAT]</Term> <Field>EDAT</Field> <Count>0</Count>
> >> <Explode>Y</Explode> </TermSet> <TermSet>
> >> <Term>2009/11/01[EDAT]</Term> <Field>EDAT</Field> <Count>0</Count>
> >> <Explode>Y</Explode> </TermSet> <OP>RANGE</OP> <OP>AND</OP>
> >> </TranslationStack><QueryTranslation>("neoplasms"[MeSH Terms] OR
> >> "neoplasms"[All Fields] OR "cancer"[All Fields]) AND 2009/10/22[EDAT] :
> >> 2009/11/01[EDAT]</QueryTranslation></eSearchResult>
> >> ^
> >>
> >> As you can see, the XML output is coming fine but the above error does
> not
> >> go..The output via this program should be just like hitting manually the
> >> above URL in the browser..
> >> The browser is Mozilla Firefox.
> >>
> >> Code:-
> >>
> >> <%@ page language = "java" %>
> >> <%@ page import = "java.sql.*" %>
> >> <%@ page import = "java.util.*" %>
> >> <%@ page import = "java.io.*" %>
> >> <%@ page import="java.lang.*" %>
> >> <%@ page import="java.net.*" %>
> >> <%@ page import="java.nio.*" %>
> >> <%@ page contentType="text/xml; charset=utf-8" pageEncoding="UTF-8" %>
> >>
> >>
> >> <%
> >>
> >> try
> >> {
> >> //String str = "<?xml version='1.0' ?>";
> >> //out.println("<?xml version='1.0' encoding='utf-8' ?>");
> >>
> >> Properties systemSettings = System.getProperties();
> >> systemSettings.put("http.proxyHost", "********");
> >> systemSettings.put("http.proxyPort", "******");
> >> systemSettings.put("sun.net.client.defaultConnectTimeout", "10000");
> >> systemSettings.put("sun.net.client.defaultReadTimeout", "10000");
> >>
> >> //out.println("Properties Set");
> >> Authenticator.setDefault(new Authenticator()
> >> {
> >> protected PasswordAuthentication getPasswordAuthentication()
> >> {
> >> return new PasswordAuthentication("**",
> >> "******".toCharArray()); // specify ur user name password of iitb login
> >> }
> >> });
> >>
> >>
> >> System.setProperties(systemSettings);
> >> //out.println("After Authentication & Properties Settings");
> >>
> >> //create xml file.
> >> //the input to google api
> >> //String textAreaContent = request.getParameter("text");
> >> String textAreaContent = "This si a tst";
> >>
> >> String str = "<?xml version='1.0' encoding='utf-8' ?>";
> >>
> >> //xml file generation ends here..
> >> //FetchDataFromNCBI_URLString.jsp
> >> String URLString = request.getParameter("txtURLString").trim();
> >>
> >> //URL url = new URL("
> >>
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=protein&term=BAA20519
> >> ");
> >> URL url = new URL(URLString); //url string taken from user input.
> >> HttpURLConnection connection = null;
> >>
> >> connection = (HttpURLConnection) url.openConnection();
> >> System.out.println("After open connection");
> >> connection.setRequestMethod("POST");
> >> connection.setDoInput(true);
> >> connection.setDoOutput(true);
> >>
> >> connection.setUseCaches(false);
> >> connection.setAllowUserInteraction(false);
> >> //connection.setFollowRedirects(true);
> >> //connection.setInstanceFollowRedirects(true);
> >> //System.out.println("Before-------------------");
> >> connection.setRequestProperty ("Content-Type","text/xml;
> >> charset=\"utf-8\"");
> >> //System.out.println("After-------------------");
> >>
> >> //System.out.println(""+ connection.getOutputStream());
> >>
> >> //System.out.println("After dataoutputstream..Line No-65");
> >>
> >> //System.out.println("Response Code="+ connection.getResponseCode);
> >>
> >> OutputStreamWriter dosout = new
> >> OutputStreamWriter(connection.getOutputStream());
> >> //System.out.println("After dosout object..Line No-63");
> >> //dosout.write(str);
> >> dosout.close ();
> >>
> >> BufferedReader in = new BufferedReader( new InputStreamReader(
> >> connection.getInputStream()));
> >>
> >> String decodedString;
> >> String tempstr = "";
> >>
> >>
> >> while ((decodedString = in.readLine()) != null)
> >> {
> >> tempstr = tempstr + decodedString;
> >> //out.println(decodedString);
> >> }
> >> out.println(tempstr);
> >> in.close();
> >> }
> >> catch(Exception ex)
> >> {
> >> out.println("Exception->"+ex);
> >> PrintWriter pw = response.getWriter();
> >> ex.printStackTrace(pw);
> >> }
> >>
> >>
> >> %>
> >>
> >> Thanks in advance..
> >>
> >> Regards,
> >> JItesh Dundas
> >>
> >> _______________________________________________
> >> Biojava-l mailing list - Biojava-l@...
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> >
>

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Re: How do I read a FASTA file containing protein sequences in lowercase?

2009-11-09T08:26:00Z

Richard (>):

> Ah OK I see what's going on.
>
> The convenience method you're using, RichSequence.IOTools.readStream(), uses
> FastaFormat to try and guess the alphabet to use based on the first line of
> the input sequence.
>
> In FastaFormat, it does this by searching for matching non-DNA symbols. The
> search is case-sensitive:
>
> protected static final Pattern aminoAcids =
> Pattern.compile(".*[FLIPQE].*");
>
> FastaFormat needs patching to make this pattern non-case-sensitive.

Patch attached.

I also took the opportunity to remove the occurrences of .* in the
Pattern above. Generally, once should be using Matcher.find() when one
is interested in matching a part of a string. This is more efficient
than using Matcher.matches() and surrounding the desired regular
expression with .*, since the latter will cause a lot of unnecessary
backtracking and make the search quadratic.

This effect only shows up for very long strings, but long strings can
and do happen in bioinformatics. The below measurements show the
quadratic behaviour of the former approach.

$ for length in 100 1000 10000 100000 1000000; do (time java
WithDotStar $length) 2>&1 | grep real; done
real 0m0.371s
real 0m0.367s
real 0m0.577s
real 0m2.735s
real 0m25.275s

$ for length in 100 1000 10000 100000 1000000; do (time java
WithoutDotStar $length) 2>&1 | grep real; done
real 0m0.309s
real 0m0.361s
real 0m0.468s
real 0m1.184s
real 0m9.703s

Kindly,
// Carl

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Re: Java Error:- XML Parsing Error: XML or text declaration not at start of entity

2009-11-08T02:22:43Z

Dear Sir,

My program is working fine and can send me an xml file with 20
records. However, it does not allow me to send large amounts of
records.

For e.g. if I enter "cancer" it will return only 20 records.

Can you please tell me what I should do next to get all those records.
Thank you in advance

Regards,
Jitesh Dundas

On Sun, Nov 1, 2009 at 9:36 PM, Andreas Prlic <andreas@...> wrote:

>
> Hi Jitesh,
>
> It is hard to read your code with all the formatting off probably due to email and many commented lines that don;t seem to get used. Can you provide the stacktrace, so we can see what part of biojava is affected?
>
> Probably a good strategy to write and debug this is to simply the problem into smaller steps. Try to first download the files you want to parse and write the code to parse them from the local file. That will avoid any issues you might encounter with networking and server/client communication. Once the parsing is working you could take it to the next step and add the server communication...
>
> Andreas
>
>
>
>
> On Sun, Nov 1, 2009 at 7:41 AM, jitesh dundas <jbdundas@...> wrote:
>>
>> Hi friends,
>>
>> I am getting this error on doing a post(using the code below) to this url->
>> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer&reldate=10
>>
>> I have written this code in .jsp file. Later I will change it into servlet.
>>
>> Error:-
>> XML Parsing Error: XML or text declaration not at start of entity
>> Location:
>> http://localhost:8080/ProteomDb/ImportFromPubmed2.jsp?txtDbName=pubmed&txtTerm=cancer&txtreldate=10&comSDay=01&comSMonth=01&txtSYear=&comEDay=01&comEMonth=01&txtEYear=&txtURLString=http%3A%2F%2Feutils.ncbi.nlm.nih.gov%2Fentrez%2Feutils%2Fesearch.fcgi%3Fdb%3Dpubmed%26term%3Dcancer%26reldate%3D10&txtsubmit=Fetch+Data+From+NCBI
>> Line Number 11, Column 1:<?xml version="1.0" ?><!DOCTYPE eSearchResult
>> PUBLIC "-//NLM//DTD eSearchResult, 11 May 2002//EN" "
>> http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd"><eSearchResult><Count>2034</Count><RetMax>20</RetMax><RetStart>0</RetStart><IdList>
>> <Id>19877350</Id> <Id>19877304</Id> <Id>19877297</Id>
>> <Id>19877284</Id> <Id>19877271</Id> <Id>19877265</Id>
>> <Id>19877250</Id> <Id>19877245</Id> <Id>19877226</Id>
>> <Id>19877210</Id> <Id>19877179</Id> <Id>19877175</Id>
>> <Id>19877161</Id> <Id>19877159</Id> <Id>19877158</Id>
>> <Id>19877123</Id> <Id>19877122</Id> <Id>19877120</Id>
>> <Id>19877119</Id> <Id>19877118</Id>
>> </IdList><TranslationSet><Translation> <From>cancer</From>
>> <To>"neoplasms"[MeSH Terms] OR "neoplasms"[All Fields] OR "cancer"[All
>> Fields]</To> </Translation></TranslationSet><TranslationStack>
>> <TermSet> <Term>"neoplasms"[MeSH Terms]</Term> <Field>MeSH
>> Terms</Field> <Count>2082133</Count> <Explode>Y</Explode>
>> </TermSet> <TermSet> <Term>"neoplasms"[All Fields]</Term> <Field>All
>> Fields</Field> <Count>1634731</Count> <Explode>Y</Explode>
>> </TermSet> <OP>OR</OP> <TermSet> <Term>"cancer"[All Fields]</Term>
>> <Field>All Fields</Field> <Count>902537</Count> <Explode>Y</Explode>
>> </TermSet> <OP>OR</OP> <OP>GROUP</OP> <TermSet>
>> <Term>2009/10/22[EDAT]</Term> <Field>EDAT</Field> <Count>0</Count>
>> <Explode>Y</Explode> </TermSet> <TermSet>
>> <Term>2009/11/01[EDAT]</Term> <Field>EDAT</Field> <Count>0</Count>
>> <Explode>Y</Explode> </TermSet> <OP>RANGE</OP> <OP>AND</OP>
>> </TranslationStack><QueryTranslation>("neoplasms"[MeSH Terms] OR
>> "neoplasms"[All Fields] OR "cancer"[All Fields]) AND 2009/10/22[EDAT] :
>> 2009/11/01[EDAT]</QueryTranslation></eSearchResult>
>> ^
>>
>> As you can see, the XML output is coming fine but the above error does not
>> go..The output via this program should be just like hitting manually the
>> above URL in the browser..
>> The browser is Mozilla Firefox.
>>
>> Code:-
>>
>> <%@ page language = "java" %>
>> <%@ page import = "java.sql.*" %>
>> <%@ page import = "java.util.*" %>
>> <%@ page import = "java.io.*" %>
>> <%@ page import="java.lang.*" %>
>> <%@ page import="java.net.*" %>
>> <%@ page import="java.nio.*" %>
>> <%@ page contentType="text/xml; charset=utf-8" pageEncoding="UTF-8" %>
>>
>>
>> <%
>>
>> try
>> {
>> //String str = "<?xml version='1.0' ?>";
>> //out.println("<?xml version='1.0' encoding='utf-8' ?>");
>>
>> Properties systemSettings = System.getProperties();
>> systemSettings.put("http.proxyHost", "********");
>> systemSettings.put("http.proxyPort", "******");
>> systemSettings.put("sun.net.client.defaultConnectTimeout", "10000");
>> systemSettings.put("sun.net.client.defaultReadTimeout", "10000");
>>
>> //out.println("Properties Set");
>> Authenticator.setDefault(new Authenticator()
>> {
>> protected PasswordAuthentication getPasswordAuthentication()
>> {
>> return new PasswordAuthentication("**",
>> "******".toCharArray()); // specify ur user name password of iitb login
>> }
>> });
>>
>>
>> System.setProperties(systemSettings);
>> //out.println("After Authentication & Properties Settings");
>>
>> //create xml file.
>> //the input to google api
>> //String textAreaContent = request.getParameter("text");
>> String textAreaContent = "This si a tst";
>>
>> String str = "<?xml version='1.0' encoding='utf-8' ?>";
>>
>> //xml file generation ends here..
>> //FetchDataFromNCBI_URLString.jsp
>> String URLString = request.getParameter("txtURLString").trim();
>>
>> //URL url = new URL("
>> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=protein&term=BAA20519
>> ");
>> URL url = new URL(URLString); //url string taken from user input.
>> HttpURLConnection connection = null;
>>
>> connection = (HttpURLConnection) url.openConnection();
>> System.out.println("After open connection");
>> connection.setRequestMethod("POST");
>> connection.setDoInput(true);
>> connection.setDoOutput(true);
>>
>> connection.setUseCaches(false);
>> connection.setAllowUserInteraction(false);
>> //connection.setFollowRedirects(true);
>> //connection.setInstanceFollowRedirects(true);
>> //System.out.println("Before-------------------");
>> connection.setRequestProperty ("Content-Type","text/xml;
>> charset=\"utf-8\"");
>> //System.out.println("After-------------------");
>>
>> //System.out.println(""+ connection.getOutputStream());
>>
>> //System.out.println("After dataoutputstream..Line No-65");
>>
>> //System.out.println("Response Code="+ connection.getResponseCode);
>>
>> OutputStreamWriter dosout = new
>> OutputStreamWriter(connection.getOutputStream());
>> //System.out.println("After dosout object..Line No-63");
>> //dosout.write(str);
>> dosout.close ();
>>
>> BufferedReader in = new BufferedReader( new InputStreamReader(
>> connection.getInputStream()));
>>
>> String decodedString;
>> String tempstr = "";
>>
>>
>> while ((decodedString = in.readLine()) != null)
>> {
>> tempstr = tempstr + decodedString;
>> //out.println(decodedString);
>> }
>> out.println(tempstr);
>> in.close();
>> }
>> catch(Exception ex)
>> {
>> out.println("Exception->"+ex);
>> PrintWriter pw = response.getWriter();
>> ex.printStackTrace(pw);
>> }
>>
>>
>> %>
>>
>> Thanks in advance..
>>
>> Regards,
>> JItesh Dundas
>>
>> _______________________________________________
>> Biojava-l mailing list - Biojava-l@...
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>

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Re: Bio Java installation inquiry

2009-11-07T22:52:00Z

Hi Andy,

At the present the plan is to spend some more time working on the modules
and then make a release (called 3.0) at some point shortly after the
hackaton in Cambridge in January. Early adopters can already now use the
modules via SVN.

Andreas

On Sat, Nov 7, 2009 at 12:21 PM, andy law (RI) <andy.law@...>wrote:

> Andreas,
>
> When will the mavenised version of biojava be officially released?
>
> Later,
>
> Andy
> ________________________________________
> From: biojava-l-bounces@... [
> biojava-l-bounces@...] On Behalf Of Andreas Prlic [
> andreas@...]
> Sent: 07 November 2009 18:14
> To: Andy Lu
> Cc: biojava-l@...
> Subject: Re: [Biojava-l] Bio Java installation inquiry
>
> Hi Andy,
>
> best thing is to download the jar files from
> http://biojava.org/wiki/BioJava:Download .
>
> Proably the easiest way to get started is to create a new project in
> eclipse
> and right click on the project-> Properties -> Java build path -> Libraries
> -> Add jars
>
> Then your project will know how where to find the dependencies and you can
> start writing your own code.
>
> Andreas
>
>
> On Sat, Nov 7, 2009 at 10:06 AM, Andy Lu <andylu0320@...> wrote:
>
> > Hi, I am able to get JMol to run on Eclipse, but I am having a lot of
> > trouble getting biojava to run, I am not sure how to set up all of the
> > class
> > path, etc.
> > I am new to using Eclipse and biojava. Is there a specific step by step
> > instruction online available?
> >
> > Any help would be greatly appreciated!
> > _______________________________________________
> > Biojava-l mailing list - Biojava-l@...
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> _______________________________________________
> Biojava-l mailing list - Biojava-l@...
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

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Re: Bio Java installation inquiry

2009-11-07T12:21:59Z

Andreas,

When will the mavenised version of biojava be officially released?

Later,

Andy
________________________________________
From: biojava-l-bounces@... [biojava-l-bounces@...] On Behalf Of Andreas Prlic [andreas@...]
Sent: 07 November 2009 18:14
To: Andy Lu
Cc: biojava-l@...
Subject: Re: [Biojava-l] Bio Java installation inquiry

Hi Andy,

best thing is to download the jar files from
http://biojava.org/wiki/BioJava:Download .

Proably the easiest way to get started is to create a new project in eclipse
and right click on the project-> Properties -> Java build path -> Libraries
-> Add jars

Then your project will know how where to find the dependencies and you can
start writing your own code.

Andreas

On Sat, Nov 7, 2009 at 10:06 AM, Andy Lu <andylu0320@...> wrote:

> Hi, I am able to get JMol to run on Eclipse, but I am having a lot of
> trouble getting biojava to run, I am not sure how to set up all of the
> class
> path, etc.
> I am new to using Eclipse and biojava. Is there a specific step by step
> instruction online available?
>
> Any help would be greatly appreciated!
> _______________________________________________
> Biojava-l mailing list - Biojava-l@...
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

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Re: Bio Java installation inquiry

2009-11-07T10:40:59Z

You don;t need to have Jmol in the classpath for running biojava, but if you
do, you can use the jmol/biojava interface contained in the protein
structure modules.
In that case JmolApplet.jar would be sufficient, you don;t need to check out
the Jmol source...

Andreas

On Sat, Nov 7, 2009 at 10:33 AM, Andy Lu <andylu0320@...> wrote:

> O I see, but don't I also need to have all of the JMol java files set up
> first, or the BioJava jar file contains everything I need?
>
>
> On Sat, Nov 7, 2009 at 1:14 PM, Andreas Prlic <andreas@...> wrote:
>
>> Hi Andy,
>>
>> best thing is to download the jar files from
>> http://biojava.org/wiki/BioJava:Download .
>>
>> Proably the easiest way to get started is to create a new project in
>> eclipse and right click on the project-> Properties -> Java build path ->
>> Libraries -> Add jars
>>
>> Then your project will know how where to find the dependencies and you
>> can start writing your own code.
>>
>> Andreas
>>
>>
>> On Sat, Nov 7, 2009 at 10:06 AM, Andy Lu <andylu0320@...> wrote:
>>
>>> Hi, I am able to get JMol to run on Eclipse, but I am having a lot of
>>> trouble getting biojava to run, I am not sure how to set up all of the
>>> class
>>> path, etc.
>>> I am new to using Eclipse and biojava. Is there a specific step by step
>>> instruction online available?
>>>
>>> Any help would be greatly appreciated!
>>> _______________________________________________
>>> Biojava-l mailing list - Biojava-l@...
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>
>>
>
>
> --
> Andy Lu
>

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