Re: Biojava-l Digest, Vol 96, Issue 5

Thanks for your input, Steve, I was able to clone the source code from the
github using a git client (SmartGit 2.02). As a note to others who may be
attempting to do the same, it took a really long time, probably about an
hour, to clone all the files, just let it keep running.

Cheers,
Matthew



> Message: 1
> Date: Thu, 6 Jan 2011 16:56:42 -0600
> From: "Steve Darnell" <[email protected]>
> Subject: Re: [Biojava-l] how to access biojava source control on svn
> To: "Sj Pookpan" <[email protected]>
> Cc: [email protected]
> Message-ID: <[email protected]>
> Content-Type: text/plain;       charset="iso-8859-1"
>
> In the past, I have had problems using the Subclipse plug-in in Eclipse to
> checkout BioJava from the svn service at github on both Windows and Mac.
>  This is how I worked around it...
>
> http://lists.open-bio.org/pipermail/biojava-dev/2010-August/004356.html
>
> The Subclipse svn plug-in from Tigris would fail during checkout with an
> exception stating "RA layer request failed svn: REPORT of '[...]' 200
> OK" for both Windows 7 and OSX 10.6.  For Windows, there are reports of
> the Windows indexing service, antivirus scanners, or the Subclipse
> JavaHL adapter causing svn problems.  Resolving these issues did not
> help.
>
> In the end, I used a git client on Windows to clone the biojava project
> from github and then imported it into Eclipse as an existing Maven
> project with the m2eclipse plug-in.
>
> --
>
> I did not revisit my search for an integrated Eclipse solution.  Now, I
> mainly use the jars made by the maven auto-build system.
>
> ~Steve
>
> -----Original Message-----
> From: [email protected] [mailto:
> [email protected]] On Behalf Of Andreas Prlic
> Sent: Wednesday, January 05, 2011 10:27 PM
> To: Sj Pookpan
> Cc: [email protected]
> Subject: Re: [Biojava-l] how to access biojava source control on svn
>
> try
>
> svn co http://svn.github.com/biojava/biojava.git ./biojava
>
>
> A
>
> On Wed, Jan 5, 2011 at 8:21 PM, Sj Pookpan <[email protected]> wrote:
> > Thank you for your answer
> > ??? I try the account mention on
> > 'http://www.biojava.org/wiki/CVS_to_SVN_Migration'
> >
> > - Anonymous SVN access or
> > - Developer SVN access (ssh account required) or
> > - BioJava SNAPSHOT builds (anonymous, Maven required)
> >
> > on eclipse SVN connection user interface, the application always ask for
> > 'password' to access 'svn', how do I get it pass?
> >
> > How ever, I already subscibe my mail to biojava mailing list (yesterday
> > 05/01/2011) and waiting for mail confirmation, but until now nothing send
> to
> > me what the next action for me.
> >
> > Regards,
> >
> > SJP.
> >
> > On 1/6/2011 12:20 AM, Marco Valtas wrote:
> >
> > You might check the Github mirror too, code.open-bio.org seem offline
> > sometimes.
> >
> > Cheers Marco.
> >
> > Sent from my iPhone
> >
> > On 05/01/2011, at 13:46, Andreas Prlic <[email protected]> wrote:
> >
> > Hi Sj,
> >
> > Better to post such questions to the public lists, otherwise they
> > might get lost...
> >
> > SVN access instructions are available from
> > http://www.biojava.org/wiki/CVS_to_SVN_Migration
> >
> > Andreas
> >
> >
> >
> >
> > 2011/1/5 Sj Pookpan <[email protected]>:
> >
> > Dear biojava master
> >
> >    I'm java developer and new to biojava, I want to know that how can get
> > access to biojava source code from SVN (by eclipse SVN).  Do I need to
> > register to biojava to get user account and password (I try to find on
> > biojava site but no where to register). Would you please give me the way
> to
> > startup this.
> >
> > SJP.
> >
> >
> >
>
> _______________________________________________
> Biojava-l mailing list  -  [email protected]
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 6 Jan 2011 16:09:29 -0800
> From: Hara Dilley <[email protected]>
> Subject: [Biojava-l] biojava3 getting the features from
>        alignedsequence
> To: "[email protected]" <[email protected]>
> Message-ID:
>        <[email protected]>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> I would like to align a set of sequences against a scaffold and get the
> list of the modifications for each aligned sequence.
> I am using biojava3
> I have tried to create a profile  thinking that I can get the
> AlignedSequences from it but that it appears to be null.
> Here is part of my code:
>
> Profile<ProteinSequence, AminoAcidCompound> profile =
> Alignments.getMultipleSequenceAlignment(lst);
> Profile.getAlignedSequence(0);
>
> Can someone please point to an example for this or to the classes I have to
> use.
> Thank you,
> Hara
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 6 Jan 2011 16:45:13 -0800
> From: Matthew Busse <[email protected]>
> Subject: [Biojava-l] Checking out code
> To: [email protected]
> Message-ID:
>        <[email protected]>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello all,
>
> I've tried several times over the past couple days to check out code from
> both of the sites, and I either receive a "Connection timed out" error from
> the code.open site or a "PROPFIND of '/biojava': 502 Bad Gateway (
> http://svn.github.com)" error from the github site.
>
> I'm using the maven and subclipse plug-ins for eclipse, and this is the
> first time Ive tried to use an SVN repository, so it's possible I'm doing
> something wrong, but these errors sound like it's a connection problem.
>
> Thanks!
>
> Matthew
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 6 Jan 2011 17:04:43 -0800
> From: Andreas Prlic <[email protected]>
> Subject: Re: [Biojava-l] Checking out code
> To: Matthew Busse <[email protected]>
> Cc: [email protected]
> Message-ID:
>        <[email protected]>
> Content-Type: text/plain; charset=ISO-8859-1
>
> I just tried to reproduce a fresh checkout from github and I can
> confirm, it does not work correctly any more.
>
> ... investigating what is going on...
>
> A
>
>
>
> On Thu, Jan 6, 2011 at 4:45 PM, Matthew Busse
> <[email protected]> wrote:
> > Hello all,
> >
> > I've tried several times over the past couple days to check out code from
> > both of the sites, and I either receive a "Connection timed out" error
> from
> > the code.open site or a "PROPFIND of '/biojava': 502 Bad Gateway (
> > http://svn.github.com)" error from the github site.
> >
> > I'm using the maven and subclipse plug-ins for eclipse, and this is the
> > first time Ive tried to use an SVN repository, so it's possible I'm doing
> > something wrong, but these errors sound like it's a connection problem.
> >
> > Thanks!
> >
> > Matthew
> > _______________________________________________
> > Biojava-l mailing list ?- [email protected]
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 6 Jan 2011 17:06:46 -0800
> From: Andreas Prlic <[email protected]>
> Subject: Re: [Biojava-l] Checking out code
> To: [email protected]
> Message-ID:
>        <[email protected]>
> Content-Type: text/plain; charset=ISO-8859-1
>
> and to follow up, I believe we are seeing this problem:
>
>
> http://support.github.com/discussions/repos/5188-fresh-checkout-of-svn-repo-shows-dozens-of-empty-files-where-they-shouldnt-be
>
>
>
>
> On Thu, Jan 6, 2011 at 5:04 PM, Andreas Prlic <[email protected]> wrote:
> > I just tried to reproduce a fresh checkout from github and I can
> > confirm, it does not work correctly any more.
> >
> > ... investigating what is going on...
> >
> > A
> >
> >
> >
> > On Thu, Jan 6, 2011 at 4:45 PM, Matthew Busse
> > <[email protected]> wrote:
> >> Hello all,
> >>
> >> I've tried several times over the past couple days to check out code
> from
> >> both of the sites, and I either receive a "Connection timed out" error
> from
> >> the code.open site or a "PROPFIND of '/biojava': 502 Bad Gateway (
> >> http://svn.github.com)" error from the github site.
> >>
> >> I'm using the maven and subclipse plug-ins for eclipse, and this is the
> >> first time Ive tried to use an SVN repository, so it's possible I'm
> doing
> >> something wrong, but these errors sound like it's a connection problem.
> >>
> >> Thanks!
> >>
> >> Matthew
> >> _______________________________________________
> >> Biojava-l mailing list ?- [email protected]
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>
> >
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 6 Jan 2011 18:24:48 -0800
> From: Andreas Prlic <[email protected]>
> Subject: [Biojava-l] github svn access issues
> To: biojava-dev <[email protected]>,
>        [email protected]
> Message-ID:
>        <[email protected]>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
>
> Seems github is currently having issues with their svn interface. As
> such if you want to get hold of a copy of the latest source for the
> moment there are the following two options:
>
> - use git rather than svn to fetch the code from github
> - use Maven and get the biojava3.0.1-SNAPSHOT builds from the
> http://www.biojava.org/download/maven/ repository
>
> Andreas
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 6 Jan 2011 21:42:50 -0500
> From: Scooter Willis <[email protected]>
> Subject: Re: [Biojava-l] biojava3 getting the features from
>        alignedsequence
> To: Hara Dilley <[email protected]>
> Cc: "[email protected]" <[email protected]>
> Message-ID:
>        <[email protected]>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hara
>
> Can you provide more of the code you are using that shows how you are
> loading the initial sequences.
>
> Thanks
>
> Scooter
>
> On Thu, Jan 6, 2011 at 7:09 PM, Hara Dilley <[email protected]> wrote:
>
> > Hi,
> >
> > I would like to align a set of sequences against a scaffold and get the
> > list of the modifications for each aligned sequence.
> > I am using biojava3
> > I have tried to create a profile  thinking that I can get the
> > AlignedSequences from it but that it appears to be null.
> > Here is part of my code:
> >
> > Profile<ProteinSequence, AminoAcidCompound> profile =
> > Alignments.getMultipleSequenceAlignment(lst);
> > Profile.getAlignedSequence(0);
> >
> > Can someone please point to an example for this or to the classes I have
> to
> > use.
> > Thank you,
> > Hara
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  [email protected]
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> >
>
>
> ------------------------------
>
> _______________________________________________
> Biojava-l mailing list  -  [email protected]
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
> End of Biojava-l Digest, Vol 96, Issue 5
> ****************************************
>
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