From tiagoantao at gmail.com  Mon Oct  3 18:12:18 2011
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Mon, 3 Oct 2011 23:12:18 +0100
Subject: [Biojava-l] VCF parser
Message-ID: <CAA9RGEOdgq9=Y5oruhjycP8Jw545rwDQG_eXKFzWKXYj2s3uQQ@mail.gmail.com>

Hi,

I wonder if there is a VCF parser in either Python or Java? Either I
am being dumb at searching (probably) or nothing exists?

Thanks,
Tiago

-- 
"If you want to get laid, go to college.? If you want an education, go
to the library." - Frank Zappa


From biojava at hannes.oib.com  Wed Oct  5 03:41:57 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 5 Oct 2011 09:41:57 +0200
Subject: [Biojava-l] NullPointerException when using
	Alignments.getMultipleSequenceAlignment
Message-ID: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com>

Hello!

I tried to follow http://biojava.org/wiki/BioJava:CookBook3:MSA, but
when I run it, I get:

java.util.concurrent.ExecutionException: java.lang.NullPointerException
	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
	at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
	at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
	at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173)

 What could I be doing wrong?

(
on the cookbook page, there is also an import missing:
import org.biojava3.alignment.Alignments;
)
-> then the cookbook runs, but my code does not

private static void processFile(String filename) {
        try {
            FileInputStream inStream = new FileInputStream(filename);
            FastaReader<DNASequence, NucleotideCompound> fastaReader =
                    new FastaReader<DNASequence, NucleotideCompound>(
                    inStream,
                    new GenericFastaHeaderParser<DNASequence,
NucleotideCompound>(),
                    new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
            LinkedHashMap<String, DNASequence> b = fastaReader.process();

            List<DNASequence> sequences = new ArrayList<DNASequence>();
            for (Entry<String, DNASequence> entry : b.entrySet()) {
                if (sequences.size() < 5) {
                    sequences.add(entry.getValue());
                }
                System.out.println(entry.getValue());
            }

            Profile<DNASequence, NucleotideCompound> profile =
Alignments.getMultipleSequenceAlignment(sequences);
            System.out.printf("Clustalw:%n%s%n", profile);

            ConcurrencyTools.shutdown();
        } catch (Exception ex) {
            Logger.getLogger(App.class.getName()).log(Level.SEVERE, null, ex);
        }
    }

From biojava at hannes.oib.com  Wed Oct  5 04:50:33 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 5 Oct 2011 10:50:33 +0200
Subject: [Biojava-l] NullPointerException when using
	Alignments.getMultipleSequenceAlignment
In-Reply-To: <CAB1D7DF.1E3D%hk3@sanger.ac.uk>
References: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com>
	<CAB1D7DF.1E3D%hk3@sanger.ac.uk>
Message-ID: <CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com>

Hi!

I read the sequence from a fasta file.

FileInputStream inStream = new FileInputStream(filename);
            FastaReader<DNASequence, NucleotideCompound> fastaReader =
                    new FastaReader<DNASequence, NucleotideCompound>(
                    inStream,
                    new GenericFastaHeaderParser<DNASequence,
NucleotideCompound>(),
                    new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
            LinkedHashMap<String, DNASequence> b = fastaReader.process();

and then use
List<DNASequence> sequences = new ArrayList<DNASequence>();
            for (Entry<String, DNASequence> entry : b.entrySet()) {
                sequences.add(entry.getValue());
}

to get the required list of DNA sequences.

I noticed in an earlier discussion, there was some talk about this too
(3-4 months ago, perhaps) and something about a possible fix in SVN.
when will it be released on the maven server?

Hannes

On Wed, Oct 5, 2011 at 10:46, Hashem Koohy <hk3 at sanger.ac.uk> wrote:
> Hi Hannes,
> It seems to me it doesn't like your ?dna Sequence!
> Is your sequence in the following format?
>
> Sequence dnaSeq = DNATools.createDNASequence("acccgggttttacagt", "id");
>
> Good luck
> Hashem
>
> On 05/10/2011 08:41, "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com>
> wrote:
>
>> Hello!
>>
>> I tried to follow http://biojava.org/wiki/BioJava:CookBook3:MSA, but
>> when I run it, I get:
>>
>> java.util.concurrent.ExecutionException: java.lang.NullPointerException
>> at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
>> at java.util.concurrent.FutureTask.get(FutureTask.java:83)
>> at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
>> at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
>> at
>> org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java
>> :173)
>>
>> ?What could I be doing wrong?
>>
>> (
>> on the cookbook page, there is also an import missing:
>> import org.biojava3.alignment.Alignments;
>> )
>> -> then the cookbook runs, but my code does not
>>
>> private static void processFile(String filename) {
>> ? ? ? ? try {
>> ? ? ? ? ? ? FileInputStream inStream = new FileInputStream(filename);
>> ? ? ? ? ? ? FastaReader<DNASequence, NucleotideCompound> fastaReader =
>> ? ? ? ? ? ? ? ? ? ? new FastaReader<DNASequence, NucleotideCompound>(
>> ? ? ? ? ? ? ? ? ? ? inStream,
>> ? ? ? ? ? ? ? ? ? ? new GenericFastaHeaderParser<DNASequence,
>> NucleotideCompound>(),
>> ? ? ? ? ? ? ? ? ? ? new
>> DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
>> ? ? ? ? ? ? LinkedHashMap<String, DNASequence> b = fastaReader.process();
>>
>> ? ? ? ? ? ? List<DNASequence> sequences = new ArrayList<DNASequence>();
>> ? ? ? ? ? ? for (Entry<String, DNASequence> entry : b.entrySet()) {
>> ? ? ? ? ? ? ? ? if (sequences.size() < 5) {
>> ? ? ? ? ? ? ? ? ? ? sequences.add(entry.getValue());
>> ? ? ? ? ? ? ? ? }
>> ? ? ? ? ? ? ? ? System.out.println(entry.getValue());
>> ? ? ? ? ? ? }
>>
>> ? ? ? ? ? ? Profile<DNASequence, NucleotideCompound> profile =
>> Alignments.getMultipleSequenceAlignment(sequences);
>> ? ? ? ? ? ? System.out.printf("Clustalw:%n%s%n", profile);
>>
>> ? ? ? ? ? ? ConcurrencyTools.shutdown();
>> ? ? ? ? } catch (Exception ex) {
>> ? ? ? ? ? ? Logger.getLogger(App.class.getName()).log(Level.SEVERE, null, ex);
>> ? ? ? ? }
>> ? ? }
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> -------------------------------
> Hashem Koohy
> PhD
> Postdoctoral Fellow,
> Sanger Institute,
> Cambridge
> Mobile: 07515425433
>
>
>
>
> --
> ?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.
>


From andreas at sdsc.edu  Wed Oct  5 13:21:19 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 5 Oct 2011 10:21:19 -0700
Subject: [Biojava-l] NullPointerException when using
	Alignments.getMultipleSequenceAlignment
In-Reply-To: <CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com>
References: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com>
	<CAB1D7DF.1E3D%hk3@sanger.ac.uk>
	<CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com>
Message-ID: <CALthepzPycvfecN9Ln8fvL6Q3PYR0HEbqfAfD9Ysa770E3dsJQ@mail.gmail.com>

Hi Hannes,

> I noticed in an earlier discussion, there was some talk about this too
> (3-4 months ago, perhaps) and something about a possible fix in SVN.
> when will it be released on the maven server?

What version are you on? We released Maven 3.0.2 just recently..

Andreas

From sbliven at ucsd.edu  Wed Oct  5 13:39:42 2011
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Wed, 5 Oct 2011 10:39:42 -0700
Subject: [Biojava-l] NullPointerException when using
	Alignments.getMultipleSequenceAlignment
In-Reply-To: <CALthepzPycvfecN9Ln8fvL6Q3PYR0HEbqfAfD9Ysa770E3dsJQ@mail.gmail.com>
References: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com>
	<CAB1D7DF.1E3D%hk3@sanger.ac.uk>
	<CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com>
	<CALthepzPycvfecN9Ln8fvL6Q3PYR0HEbqfAfD9Ysa770E3dsJQ@mail.gmail.com>
Message-ID: <CA+P6arkm11zAB3du8JVKxcEGh-5XXqFKMpsVa8W6w6qxAVcSLA@mail.gmail.com>

In the current SVN code (and therefor probably Biojava 3.0.2),
CookbookMSA.java includes that import statement but is otherwise identical
to the wiki version. It runs just fine for me. Probably updating to Biojava
3.0.2 will fix the null pointer exception.

This does highlight the problem of keeping the wiki synchronized with the
current BioJava version. Ideally, part of the release process could include
automated updating of the wiki cookbook from the SVN code, with older
versions available as a reference. However, I'm not sure that anyone would
be willing to set up such a complex release process.

-Spencer

On Wed, Oct 5, 2011 at 10:21, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi Hannes,
>
> > I noticed in an earlier discussion, there was some talk about this too
> > (3-4 months ago, perhaps) and something about a possible fix in SVN.
> > when will it be released on the maven server?
>
> What version are you on? We released Maven 3.0.2 just recently..
>
> Andreas
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From amr_alhossary at hotmail.com  Wed Oct  5 14:26:16 2011
From: amr_alhossary at hotmail.com (Amr AL-Hossary)
Date: Wed, 5 Oct 2011 20:26:16 +0200
Subject: [Biojava-l] NullPointerException when
	usingAlignments.getMultipleSequenceAlignment
In-Reply-To: <CA+P6arkm11zAB3du8JVKxcEGh-5XXqFKMpsVa8W6w6qxAVcSLA@mail.gmail.com>
References: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com><CAB1D7DF.1E3D%hk3@sanger.ac.uk><CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com><CALthepzPycvfecN9Ln8fvL6Q3PYR0HEbqfAfD9Ysa770E3dsJQ@mail.gmail.com>
	<CA+P6arkm11zAB3du8JVKxcEGh-5XXqFKMpsVa8W6w6qxAVcSLA@mail.gmail.com>
Message-ID: <BLU150-ds52105839586554A9B29258EF80@phx.gbl>

I agree with you 100%.

I have met problems this week in working with the SPICE code too, to the 
extent that I delayed the whole idea till I have more suitable time to 
reimplement it myself.

Amr

--------------------------------------------------
From: "Spencer Bliven" <sbliven at ucsd.edu>
Sent: Wednesday, October 05, 2011 7:39 PM
To: "Andreas Prlic" <andreas at sdsc.edu>
Cc: <biojava-l at lists.open-bio.org>
Subject: Re: [Biojava-l] NullPointerException when 
usingAlignments.getMultipleSequenceAlignment

> In the current SVN code (and therefor probably Biojava 3.0.2),
> CookbookMSA.java includes that import statement but is otherwise identical
> to the wiki version. It runs just fine for me. Probably updating to 
> Biojava
> 3.0.2 will fix the null pointer exception.
>
> This does highlight the problem of keeping the wiki synchronized with the
> current BioJava version. Ideally, part of the release process could 
> include
> automated updating of the wiki cookbook from the SVN code, with older
> versions available as a reference. However, I'm not sure that anyone would
> be willing to set up such a complex release process.
>
> -Spencer
>
> On Wed, Oct 5, 2011 at 10:21, Andreas Prlic <andreas at sdsc.edu> wrote:
>
>> Hi Hannes,
>>
>> > I noticed in an earlier discussion, there was some talk about this too
>> > (3-4 months ago, perhaps) and something about a possible fix in SVN.
>> > when will it be released on the maven server?
>>
>> What version are you on? We released Maven 3.0.2 just recently..
>>
>> Andreas
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

From biojava at hannes.oib.com  Wed Oct  5 15:22:13 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 5 Oct 2011 21:22:13 +0200
Subject: [Biojava-l] NullPointerException when using
	Alignments.getMultipleSequenceAlignment
In-Reply-To: <CA+P6arkm11zAB3du8JVKxcEGh-5XXqFKMpsVa8W6w6qxAVcSLA@mail.gmail.com>
References: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com>
	<CAB1D7DF.1E3D%hk3@sanger.ac.uk>
	<CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com>
	<CALthepzPycvfecN9Ln8fvL6Q3PYR0HEbqfAfD9Ysa770E3dsJQ@mail.gmail.com>
	<CA+P6arkm11zAB3du8JVKxcEGh-5XXqFKMpsVa8W6w6qxAVcSLA@mail.gmail.com>
Message-ID: <CAPXi2m=gHua1ZThqSFE+_zcP-KoCtT1dZ2hsD3sDZQgG6Bvynw@mail.gmail.com>

2011/10/5 Spencer Bliven <sbliven at ucsd.edu>:
> In the current SVN code (and therefor probably Biojava 3.0.2),
> CookbookMSA.java includes that import statement but is otherwise identical
> to the wiki version. It runs just fine for me. Probably updating to Biojava
> 3.0.2 will fix the null pointer exception.

I installed it via Maven just last week - so I guess it should be on
3.0.2 - I'll check tomorrow.

Anyhow, the problem isn't the wiki (I already updated that, btw) but
the fact that it seems to work with Protein Sequences, but when I use
my DNA sequences, it breaks.
If you go to my first post, I copied my code there (just add a wrapper
main that supplies a valid fasta file as parameter)

Hannes

From andreas at sdsc.edu  Wed Oct  5 15:30:41 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 5 Oct 2011 12:30:41 -0700
Subject: [Biojava-l] NullPointerException when using
	Alignments.getMultipleSequenceAlignment
In-Reply-To: <CAPXi2m=gHua1ZThqSFE+_zcP-KoCtT1dZ2hsD3sDZQgG6Bvynw@mail.gmail.com>
References: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com>
	<CAB1D7DF.1E3D%hk3@sanger.ac.uk>
	<CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com>
	<CALthepzPycvfecN9Ln8fvL6Q3PYR0HEbqfAfD9Ysa770E3dsJQ@mail.gmail.com>
	<CA+P6arkm11zAB3du8JVKxcEGh-5XXqFKMpsVa8W6w6qxAVcSLA@mail.gmail.com>
	<CAPXi2m=gHua1ZThqSFE+_zcP-KoCtT1dZ2hsD3sDZQgG6Bvynw@mail.gmail.com>
Message-ID: <CALthepyBzyVUFG0+gDgrgGAXBoY7jM=F4T_1D7xZbSscaXRd2g@mail.gmail.com>

Can you provide the fasta file? otherwise this is difficult to reproduce...

Andreas

On Wed, Oct 5, 2011 at 12:22 PM, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> 2011/10/5 Spencer Bliven <sbliven at ucsd.edu>:
>> In the current SVN code (and therefor probably Biojava 3.0.2),
>> CookbookMSA.java includes that import statement but is otherwise identical
>> to the wiki version. It runs just fine for me. Probably updating to Biojava
>> 3.0.2 will fix the null pointer exception.
>
> I installed it via Maven just last week - so I guess it should be on
> 3.0.2 - I'll check tomorrow.
>
> Anyhow, the problem isn't the wiki (I already updated that, btw) but
> the fact that it seems to work with Protein Sequences, but when I use
> my DNA sequences, it breaks.
> If you go to my first post, I copied my code there (just add a wrapper
> main that supplies a valid fasta file as parameter)
>
> Hannes
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From biojava at hannes.oib.com  Wed Oct  5 15:34:38 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 5 Oct 2011 21:34:38 +0200
Subject: [Biojava-l] NullPointerException when using
	Alignments.getMultipleSequenceAlignment
In-Reply-To: <CALthepyBzyVUFG0+gDgrgGAXBoY7jM=F4T_1D7xZbSscaXRd2g@mail.gmail.com>
References: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com>
	<CAB1D7DF.1E3D%hk3@sanger.ac.uk>
	<CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com>
	<CALthepzPycvfecN9Ln8fvL6Q3PYR0HEbqfAfD9Ysa770E3dsJQ@mail.gmail.com>
	<CA+P6arkm11zAB3du8JVKxcEGh-5XXqFKMpsVa8W6w6qxAVcSLA@mail.gmail.com>
	<CAPXi2m=gHua1ZThqSFE+_zcP-KoCtT1dZ2hsD3sDZQgG6Bvynw@mail.gmail.com>
	<CALthepyBzyVUFG0+gDgrgGAXBoY7jM=F4T_1D7xZbSscaXRd2g@mail.gmail.com>
Message-ID: <CAPXi2m=BY2uym5hggHh75rU9o36LLV9276uFDQQ96xwdsa098w@mail.gmail.com>

On Wed, Oct 5, 2011 at 21:30, Andreas Prlic <andreas at sdsc.edu> wrote:
> Can you provide the fasta file? otherwise this is difficult to reproduce...
>
> Andreas

Unfortunately, the files in question are under NDA - does it work with
other fasta files? I could not get it to work with the files I tried.

Hannes

From andreas at sdsc.edu  Wed Oct  5 20:29:11 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 5 Oct 2011 17:29:11 -0700
Subject: [Biojava-l] NullPointerException when using
	Alignments.getMultipleSequenceAlignment
In-Reply-To: <CAPXi2m=BY2uym5hggHh75rU9o36LLV9276uFDQQ96xwdsa098w@mail.gmail.com>
References: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com>
	<CAB1D7DF.1E3D%hk3@sanger.ac.uk>
	<CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com>
	<CALthepzPycvfecN9Ln8fvL6Q3PYR0HEbqfAfD9Ysa770E3dsJQ@mail.gmail.com>
	<CA+P6arkm11zAB3du8JVKxcEGh-5XXqFKMpsVa8W6w6qxAVcSLA@mail.gmail.com>
	<CAPXi2m=gHua1ZThqSFE+_zcP-KoCtT1dZ2hsD3sDZQgG6Bvynw@mail.gmail.com>
	<CALthepyBzyVUFG0+gDgrgGAXBoY7jM=F4T_1D7xZbSscaXRd2g@mail.gmail.com>
	<CAPXi2m=BY2uym5hggHh75rU9o36LLV9276uFDQQ96xwdsa098w@mail.gmail.com>
Message-ID: <CALthepwAgkbSdyicc=tP1CwzVsXGypN0FPc+kGGvuKgkecq7wA@mail.gmail.com>

> Unfortunately, the files in question are under NDA - does it work with
> other fasta files? I could not get it to work with the files I tried.

I just wrote a junit test for DNA alignments and it works for me. DNA
alignments by default are using the nuc-4_4 substitution matrix for
the alignment. It contains the following  columns.    A   T   G   C
S   W   R   Y   K   M   B   V   H   D   N

Does your FASTA file contain any characters that are not in this list?

Andreas

From biojava at hannes.oib.com  Thu Oct  6 03:32:59 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 6 Oct 2011 09:32:59 +0200
Subject: [Biojava-l] losing meta-info after multiple sequence alignment
Message-ID: <CAPXi2mn-tbGzpShDiYD=ghCo123_a4iM5TPnRsBjnbCNHFd9Bg@mail.gmail.com>

Hi again!

So, my MSA is now working, thanks for the help so far.

What I ran into now is that most of the meta-information of a Sequence
seems to get lost during the MSA step.

e.g.:
I'd like to attach the string from the fasta file (description,
header, whatever it is called) to the sequence and keep it attached
for further use after the MSA step.

1) shouldn't the fasta reader automatically populate this info? which
is the correct field (OriginalHeader or Description or something
else)?
2) the MSA step seems to throw away all meta info. I attached the
string as OriginalHeader before starting the MSA, and afterwards it is
"null"

Thanks,
Hannes

From biojava at hannes.oib.com  Thu Oct  6 04:07:17 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 6 Oct 2011 10:07:17 +0200
Subject: [Biojava-l] losing meta-info after multiple sequence alignment
In-Reply-To: <CAPXi2mn-tbGzpShDiYD=ghCo123_a4iM5TPnRsBjnbCNHFd9Bg@mail.gmail.com>
References: <CAPXi2mn-tbGzpShDiYD=ghCo123_a4iM5TPnRsBjnbCNHFd9Bg@mail.gmail.com>
Message-ID: <CAPXi2mm4WAYrLFMnAcU7iB+oezS=GXqCEbsdwZXTgbW=7_GS3w@mail.gmail.com>

On Thu, Oct 6, 2011 at 09:32, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> Hi again!
> What I ran into now is that most of the meta-information of a Sequence
> seems to get lost during the MSA step.

Okay, that was something caused by following another cookbook script
(that, unfortunately, has absolutely no docs or comments) - I found
the getOriginalSequence() method, can work with that. Thanks!

Hannes


From biojava at hannes.oib.com  Thu Oct  6 06:37:23 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 6 Oct 2011 12:37:23 +0200
Subject: [Biojava-l] losing meta-info after multiple sequence alignment
In-Reply-To: <CAB2FB9A.F0E0%hwillis@scripps.edu>
References: <CAPXi2mm4WAYrLFMnAcU7iB+oezS=GXqCEbsdwZXTgbW=7_GS3w@mail.gmail.com>
	<CAB2FB9A.F0E0%hwillis@scripps.edu>
Message-ID: <CAPXi2mk=Zomg3HmxBET3b95ujJW8-UBfawJ0byPVWUXrMf5Sbg@mail.gmail.com>

Thanks, I'll try to add what I find out. It's a wiki after all. I'll
just ask the mailing list if things are unclear before I add stuff to
the wiki.

One thing that bugged me just now, and since I can't find documentation on it:

Why is a sequence indexed by 1-(n+1) instead of 0-n? That's rather
un-java-like, especially since you just get an OutOfBoundsException,
and the range is not specified in the javadoc, or I could not find it
easily in the complex class hierarchy.

Hannes

2011/10/6 Scooter Willis <HWillis at scripps.edu>:
> Hannes
>
> As you can tell we need to improve the cookbook examples. Since you are
> going through that process would welcome any contributions you can make.
>
> Thanks
>
> Scooter
>
> On 10/6/11 4:07 AM, "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com>
> wrote:
>
>>On Thu, Oct 6, 2011 at 09:32, Hannes Brandst?tter-M?ller
>><biojava at hannes.oib.com> wrote:
>>> Hi again!
>>> What I ran into now is that most of the meta-information of a Sequence
>>> seems to get lost during the MSA step.
>>
>>Okay, that was something caused by following another cookbook script
>>(that, unfortunately, has absolutely no docs or comments) - I found
>>the getOriginalSequence() method, can work with that. Thanks!
>>
>>Hannes
>>
>>_______________________________________________
>>Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>


From HWillis at scripps.edu  Thu Oct  6 06:32:10 2011
From: HWillis at scripps.edu (Scooter Willis)
Date: Thu, 6 Oct 2011 06:32:10 -0400
Subject: [Biojava-l] losing meta-info after multiple sequence alignment
In-Reply-To: <CAPXi2mm4WAYrLFMnAcU7iB+oezS=GXqCEbsdwZXTgbW=7_GS3w@mail.gmail.com>
Message-ID: <CAB2FB9A.F0E0%hwillis@scripps.edu>

Hannes

As you can tell we need to improve the cookbook examples. Since you are
going through that process would welcome any contributions you can make.

Thanks

Scooter

On 10/6/11 4:07 AM, "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com>
wrote:

>On Thu, Oct 6, 2011 at 09:32, Hannes Brandst?tter-M?ller
><biojava at hannes.oib.com> wrote:
>> Hi again!
>> What I ran into now is that most of the meta-information of a Sequence
>> seems to get lost during the MSA step.
>
>Okay, that was something caused by following another cookbook script
>(that, unfortunately, has absolutely no docs or comments) - I found
>the getOriginalSequence() method, can work with that. Thanks!
>
>Hannes
>
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/biojava-l



From andreas.prlic at gmail.com  Thu Oct  6 11:35:22 2011
From: andreas.prlic at gmail.com (Andreas Prlic)
Date: Thu, 6 Oct 2011 08:35:22 -0700
Subject: [Biojava-l] BioJava Help
In-Reply-To: <CA+ggGe4Efh5c8-FFFE3hS12E-4ergVcBBn2FQvT1juZTSUmpng@mail.gmail.com>
References: <CA+ggGe4Efh5c8-FFFE3hS12E-4ergVcBBn2FQvT1juZTSUmpng@mail.gmail.com>
Message-ID: <CALthepw8W_T0B9dSAqQOnFU1UnZjLUhqS-8dVoKd60xB9SpmCA@mail.gmail.com>

Hi Omer,

We are having problems with the anonymous SVN server quite often. I
recommend trying the git copy at github, or their SVN interface, or
using Maven to install it.

http://www.biojava.org/wiki/CVS_to_SVN_Migration

Andreas

On Thu, Oct 6, 2011 at 1:56 AM, Omer Eilam <omereila at post.tau.ac.il> wrote:
> Dear Andreas,
>
> I wish to install BioJava for my eclipse IDE.
> I followed all the instructions in the website
> http://www.biojava.org/wiki/BioJava3_eclipse.
> I currently have problems with the last step. I create a new Maven
> project, but when I try to type /biojava/biojava-live/trunk in the SCM
> URL, I get an "invalid URL" error.
> Please let me know what seems to be the problem and how can I fix it.
>
> Thanks much!
> omer
>
> --
> Omer Eilam
> Complex Network Systems
> Prof. Eytan Ruppin
> Tel-Aviv University
> http://cns.cs.tau.ac.il/
>

From sbliven at ucsd.edu  Thu Oct  6 14:29:06 2011
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Thu, 6 Oct 2011 11:29:06 -0700
Subject: [Biojava-l] losing meta-info after multiple sequence alignment
In-Reply-To: <CAPXi2mk=Zomg3HmxBET3b95ujJW8-UBfawJ0byPVWUXrMf5Sbg@mail.gmail.com>
References: <CAPXi2mm4WAYrLFMnAcU7iB+oezS=GXqCEbsdwZXTgbW=7_GS3w@mail.gmail.com>
	<CAB2FB9A.F0E0%hwillis@scripps.edu>
	<CAPXi2mk=Zomg3HmxBET3b95ujJW8-UBfawJ0byPVWUXrMf5Sbg@mail.gmail.com>
Message-ID: <CA+P6arkEx4RTGWo=HadaCX1v41FBv-CiPUudq7LLo+ooOCXR9Q@mail.gmail.com>

I think that 1-based indexing was chosen because that's what's used in
genome databases like GenBank. Thus gene offsets from outside data sources
can be used directly without subtracting 1. That said, almost every time I
write code using sequences I get off-by-one errors, so I understand your
frustration. We should definitely improve documentation so that every method
that takes 1-based indexes are clearly marked.

-Spencer

On Thu, Oct 6, 2011 at 03:37, Hannes Brandst?tter-M?ller <
biojava at hannes.oib.com> wrote:

> Thanks, I'll try to add what I find out. It's a wiki after all. I'll
> just ask the mailing list if things are unclear before I add stuff to
> the wiki.
>
> One thing that bugged me just now, and since I can't find documentation on
> it:
>
> Why is a sequence indexed by 1-(n+1) instead of 0-n? That's rather
> un-java-like, especially since you just get an OutOfBoundsException,
> and the range is not specified in the javadoc, or I could not find it
> easily in the complex class hierarchy.
>
> Hannes
>
> 2011/10/6 Scooter Willis <HWillis at scripps.edu>:
> > Hannes
> >
> > As you can tell we need to improve the cookbook examples. Since you are
> > going through that process would welcome any contributions you can make.
> >
> > Thanks
> >
> > Scooter
> >
> > On 10/6/11 4:07 AM, "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com
> >
> > wrote:
> >
> >>On Thu, Oct 6, 2011 at 09:32, Hannes Brandst?tter-M?ller
> >><biojava at hannes.oib.com> wrote:
> >>> Hi again!
> >>> What I ran into now is that most of the meta-information of a Sequence
> >>> seems to get lost during the MSA step.
> >>
> >>Okay, that was something caused by following another cookbook script
> >>(that, unfortunately, has absolutely no docs or comments) - I found
> >>the getOriginalSequence() method, can work with that. Thanks!
> >>
> >>Hannes
> >>
> >>_______________________________________________
> >>Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> >
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From andreas.prlic at gmail.com  Sun Oct  9 21:58:43 2011
From: andreas.prlic at gmail.com (Andreas Prlic)
Date: Sun, 9 Oct 2011 18:58:43 -0700
Subject: [Biojava-l] BioJava Help
In-Reply-To: <CA+ggGe7U1VevV+R7gyW1gFxns-zjke86F=h450z0XsRywzLtMw@mail.gmail.com>
References: <CA+ggGe4Efh5c8-FFFE3hS12E-4ergVcBBn2FQvT1juZTSUmpng@mail.gmail.com>
	<CALthepw8W_T0B9dSAqQOnFU1UnZjLUhqS-8dVoKd60xB9SpmCA@mail.gmail.com>
	<CA+ggGe7U1VevV+R7gyW1gFxns-zjke86F=h450z0XsRywzLtMw@mail.gmail.com>
Message-ID: <CALthepyXMb9uy72cw-ORaBGnUf6LvuEHrurY+y2_4GaduvjE_A@mail.gmail.com>

Hi Omer,

Our recommendation nowadays for working with Blast is to get XML
output and simply parse that. Depending on what you need that will
give you more details than the parser that is in the BioJava 1.8
(legacy) project. (if you still want to give that one a try, there is
a cookbook page for it)

Andreas


On Sun, Oct 9, 2011 at 2:26 AM, Omer Eilam <omereila at post.tau.ac.il> wrote:
> I eventually succeeded in importing Biojava.
> I read in the paper that there is a parser for BLAST - where can I get
> more information/API on this?
>
> Thanks!
> omer
>
> On Thu, Oct 6, 2011 at 5:35 PM, Andreas Prlic <andreas.prlic at gmail.com> wrote:
>> Hi Omer,
>>
>> We are having problems with the anonymous SVN server quite often. I
>> recommend trying the git copy at github, or their SVN interface, or
>> using Maven to install it.
>>
>> http://www.biojava.org/wiki/CVS_to_SVN_Migration
>>
>> Andreas
>>
>> On Thu, Oct 6, 2011 at 1:56 AM, Omer Eilam <omereila at post.tau.ac.il> wrote:
>>> Dear Andreas,
>>>
>>> I wish to install BioJava for my eclipse IDE.
>>> I followed all the instructions in the website
>>> http://www.biojava.org/wiki/BioJava3_eclipse.
>>> I currently have problems with the last step. I create a new Maven
>>> project, but when I try to type /biojava/biojava-live/trunk in the SCM
>>> URL, I get an "invalid URL" error.
>>> Please let me know what seems to be the problem and how can I fix it.
>>>
>>> Thanks much!
>>> omer
>>>
>>> --
>>> Omer Eilam
>>> Complex Network Systems
>>> Prof. Eytan Ruppin
>>> Tel-Aviv University
>>> http://cns.cs.tau.ac.il/
>>>
>>
>
>
>
> --
> Omer Eilam
> Complex Network Systems
> Prof. Eytan Ruppin
> Tel-Aviv University
> http://cns.cs.tau.ac.il/
>

From shakunb at uom.ac.mu  Mon Oct 10 05:03:34 2011
From: shakunb at uom.ac.mu (Shakuntala Baichoo)
Date: Mon, 10 Oct 2011 13:03:34 +0400
Subject: [Biojava-l] Biojava-l Digest, Vol 105, Issue 5
In-Reply-To: <mailman.7.1318003203.13809.biojava-l@lists.open-bio.org>
References: <mailman.7.1318003203.13809.biojava-l@lists.open-bio.org>
Message-ID: <CAKpuL5gkmSQk3hJSnDdSRqovmnu3x_BaNPG1evLT7p5ugRLA7Q@mail.gmail.com>

Does anyone know how to find codon usage from data in a genbank file or embl
file.

Thanks
Shakun

On Fri, Oct 7, 2011 at 8:00 PM, <biojava-l-request at lists.open-bio.org>wrote:

> Send Biojava-l mailing list submissions to
>        biojava-l at lists.open-bio.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://lists.open-bio.org/mailman/listinfo/biojava-l
> or, via email, send a message with subject or body 'help' to
>        biojava-l-request at lists.open-bio.org
>
> You can reach the person managing the list at
>        biojava-l-owner at lists.open-bio.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Biojava-l digest..."
>
>
> Today's Topics:
>
>   1. Re: losing meta-info after multiple sequence alignment
>      (Spencer Bliven)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 6 Oct 2011 11:29:06 -0700
> From: Spencer Bliven <sbliven at ucsd.edu>
> Subject: Re: [Biojava-l] losing meta-info after multiple sequence
>        alignment
> To: Hannes Brandst?tter-M?ller <biojava at hannes.oib.com>
> Cc: "Biojava-l at lists.open-bio.org" <biojava-l at lists.open-bio.org>,
>        Scooter Willis <HWillis at scripps.edu>
> Message-ID:
>        <CA+P6arkEx4RTGWo=HadaCX1v41FBv-CiPUudq7LLo+ooOCXR9Q at mail.gmail.com
> >
> Content-Type: text/plain; charset=UTF-8
>
> I think that 1-based indexing was chosen because that's what's used in
> genome databases like GenBank. Thus gene offsets from outside data sources
> can be used directly without subtracting 1. That said, almost every time I
> write code using sequences I get off-by-one errors, so I understand your
> frustration. We should definitely improve documentation so that every
> method
> that takes 1-based indexes are clearly marked.
>
> -Spencer
>
> On Thu, Oct 6, 2011 at 03:37, Hannes Brandst?tter-M?ller <
> biojava at hannes.oib.com> wrote:
>
> > Thanks, I'll try to add what I find out. It's a wiki after all. I'll
> > just ask the mailing list if things are unclear before I add stuff to
> > the wiki.
> >
> > One thing that bugged me just now, and since I can't find documentation
> on
> > it:
> >
> > Why is a sequence indexed by 1-(n+1) instead of 0-n? That's rather
> > un-java-like, especially since you just get an OutOfBoundsException,
> > and the range is not specified in the javadoc, or I could not find it
> > easily in the complex class hierarchy.
> >
> > Hannes
> >
> > 2011/10/6 Scooter Willis <HWillis at scripps.edu>:
> > > Hannes
> > >
> > > As you can tell we need to improve the cookbook examples. Since you are
> > > going through that process would welcome any contributions you can
> make.
> > >
> > > Thanks
> > >
> > > Scooter
> > >
> > > On 10/6/11 4:07 AM, "Hannes Brandst?tter-M?ller" <
> biojava at hannes.oib.com
> > >
> > > wrote:
> > >
> > >>On Thu, Oct 6, 2011 at 09:32, Hannes Brandst?tter-M?ller
> > >><biojava at hannes.oib.com> wrote:
> > >>> Hi again!
> > >>> What I ran into now is that most of the meta-information of a
> Sequence
> > >>> seems to get lost during the MSA step.
> > >>
> > >>Okay, that was something caused by following another cookbook script
> > >>(that, unfortunately, has absolutely no docs or comments) - I found
> > >>the getOriginalSequence() method, can work with that. Thanks!
> > >>
> > >>Hannes
> > >>
> > >>_______________________________________________
> > >>Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > >>http://lists.open-bio.org/mailman/listinfo/biojava-l
> > >
> > >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
>
>
> ------------------------------
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
> End of Biojava-l Digest, Vol 105, Issue 5
> *****************************************
>

Email Disclaimer:
This email and all its contents are subject to the disclaimer at http://www.uom.ac.mu/emaildisclaimer  


From tariq_cp at hotmail.com  Mon Oct 10 12:27:27 2011
From: tariq_cp at hotmail.com (Muhammad Tariq Pervez)
Date: Mon, 10 Oct 2011 16:27:27 +0000
Subject: [Biojava-l] Biojava-l Digest, Vol 105, Issue 2
In-Reply-To: <mailman.3.1317830404.30987.biojava-l@lists.open-bio.org>
References: <mailman.3.1317830404.30987.biojava-l@lists.open-bio.org>
Message-ID: <SNT131-W377F9853A3A2D61396BF30FCFD0@phx.gbl>


Yes, the issue was also faced by me. 
I also highlighted the solution.

The solution has also been uploaded/updated in SVN.


Muhammad Tariq Pervez

PhD Scholar


> From: biojava-l-request at lists.open-bio.org
> Subject: Biojava-l Digest, Vol 105, Issue 2
> To: biojava-l at lists.open-bio.org
> Date: Wed, 5 Oct 2011 12:00:04 -0400
> 
> Send Biojava-l mailing list submissions to
> 	biojava-l at lists.open-bio.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://lists.open-bio.org/mailman/listinfo/biojava-l
> or, via email, send a message with subject or body 'help' to
> 	biojava-l-request at lists.open-bio.org
> 
> You can reach the person managing the list at
> 	biojava-l-owner at lists.open-bio.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Biojava-l digest..."
> 
> 
> Today's Topics:
> 
>    1. NullPointerException when using
>       Alignments.getMultipleSequenceAlignment (Hannes Brandst?tter-M?ller)
>    2. Re: NullPointerException when using
>       Alignments.getMultipleSequenceAlignment (Hannes Brandst?tter-M?ller)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 5 Oct 2011 09:41:57 +0200
> From: Hannes Brandst?tter-M?ller 	<biojava at hannes.oib.com>
> Subject: [Biojava-l] NullPointerException when using
> 	Alignments.getMultipleSequenceAlignment
> To: biojava-l at lists.open-bio.org
> Message-ID:
> 	<CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hello!
> 
> I tried to follow http://biojava.org/wiki/BioJava:CookBook3:MSA, but
> when I run it, I get:
> 
> java.util.concurrent.ExecutionException: java.lang.NullPointerException
> 	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
> 	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
> 	at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
> 	at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
> 	at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173)
> 
>  What could I be doing wrong?
> 
> (
> on the cookbook page, there is also an import missing:
> import org.biojava3.alignment.Alignments;
> )
> -> then the cookbook runs, but my code does not
> 
> private static void processFile(String filename) {
>         try {
>             FileInputStream inStream = new FileInputStream(filename);
>             FastaReader<DNASequence, NucleotideCompound> fastaReader =
>                     new FastaReader<DNASequence, NucleotideCompound>(
>                     inStream,
>                     new GenericFastaHeaderParser<DNASequence,
> NucleotideCompound>(),
>                     new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
>             LinkedHashMap<String, DNASequence> b = fastaReader.process();
> 
>             List<DNASequence> sequences = new ArrayList<DNASequence>();
>             for (Entry<String, DNASequence> entry : b.entrySet()) {
>                 if (sequences.size() < 5) {
>                     sequences.add(entry.getValue());
>                 }
>                 System.out.println(entry.getValue());
>             }
> 
>             Profile<DNASequence, NucleotideCompound> profile =
> Alignments.getMultipleSequenceAlignment(sequences);
>             System.out.printf("Clustalw:%n%s%n", profile);
> 
>             ConcurrencyTools.shutdown();
>         } catch (Exception ex) {
>             Logger.getLogger(App.class.getName()).log(Level.SEVERE, null, ex);
>         }
>     }
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Wed, 5 Oct 2011 10:50:33 +0200
> From: Hannes Brandst?tter-M?ller 	<biojava at hannes.oib.com>
> Subject: Re: [Biojava-l] NullPointerException when using
> 	Alignments.getMultipleSequenceAlignment
> To: biojava-l at lists.open-bio.org
> Message-ID:
> 	<CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi!
> 
> I read the sequence from a fasta file.
> 
> FileInputStream inStream = new FileInputStream(filename);
>             FastaReader<DNASequence, NucleotideCompound> fastaReader =
>                     new FastaReader<DNASequence, NucleotideCompound>(
>                     inStream,
>                     new GenericFastaHeaderParser<DNASequence,
> NucleotideCompound>(),
>                     new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
>             LinkedHashMap<String, DNASequence> b = fastaReader.process();
> 
> and then use
> List<DNASequence> sequences = new ArrayList<DNASequence>();
>             for (Entry<String, DNASequence> entry : b.entrySet()) {
>                 sequences.add(entry.getValue());
> }
> 
> to get the required list of DNA sequences.
> 
> I noticed in an earlier discussion, there was some talk about this too
> (3-4 months ago, perhaps) and something about a possible fix in SVN.
> when will it be released on the maven server?
> 
> Hannes
> 
> On Wed, Oct 5, 2011 at 10:46, Hashem Koohy <hk3 at sanger.ac.uk> wrote:
> > Hi Hannes,
> > It seems to me it doesn't like your ?dna Sequence!
> > Is your sequence in the following format?
> >
> > Sequence dnaSeq = DNATools.createDNASequence("acccgggttttacagt", "id");
> >
> > Good luck
> > Hashem
> >
> > On 05/10/2011 08:41, "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com>
> > wrote:
> >
> >> Hello!
> >>
> >> I tried to follow http://biojava.org/wiki/BioJava:CookBook3:MSA, but
> >> when I run it, I get:
> >>
> >> java.util.concurrent.ExecutionException: java.lang.NullPointerException
> >> at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
> >> at java.util.concurrent.FutureTask.get(FutureTask.java:83)
> >> at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
> >> at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
> >> at
> >> org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java
> >> :173)
> >>
> >> ?What could I be doing wrong?
> >>
> >> (
> >> on the cookbook page, there is also an import missing:
> >> import org.biojava3.alignment.Alignments;
> >> )
> >> -> then the cookbook runs, but my code does not
> >>
> >> private static void processFile(String filename) {
> >> ? ? ? ? try {
> >> ? ? ? ? ? ? FileInputStream inStream = new FileInputStream(filename);
> >> ? ? ? ? ? ? FastaReader<DNASequence, NucleotideCompound> fastaReader =
> >> ? ? ? ? ? ? ? ? ? ? new FastaReader<DNASequence, NucleotideCompound>(
> >> ? ? ? ? ? ? ? ? ? ? inStream,
> >> ? ? ? ? ? ? ? ? ? ? new GenericFastaHeaderParser<DNASequence,
> >> NucleotideCompound>(),
> >> ? ? ? ? ? ? ? ? ? ? new
> >> DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
> >> ? ? ? ? ? ? LinkedHashMap<String, DNASequence> b = fastaReader.process();
> >>
> >> ? ? ? ? ? ? List<DNASequence> sequences = new ArrayList<DNASequence>();
> >> ? ? ? ? ? ? for (Entry<String, DNASequence> entry : b.entrySet()) {
> >> ? ? ? ? ? ? ? ? if (sequences.size() < 5) {
> >> ? ? ? ? ? ? ? ? ? ? sequences.add(entry.getValue());
> >> ? ? ? ? ? ? ? ? }
> >> ? ? ? ? ? ? ? ? System.out.println(entry.getValue());
> >> ? ? ? ? ? ? }
> >>
> >> ? ? ? ? ? ? Profile<DNASequence, NucleotideCompound> profile =
> >> Alignments.getMultipleSequenceAlignment(sequences);
> >> ? ? ? ? ? ? System.out.printf("Clustalw:%n%s%n", profile);
> >>
> >> ? ? ? ? ? ? ConcurrencyTools.shutdown();
> >> ? ? ? ? } catch (Exception ex) {
> >> ? ? ? ? ? ? Logger.getLogger(App.class.getName()).log(Level.SEVERE, null, ex);
> >> ? ? ? ? }
> >> ? ? }
> >> _______________________________________________
> >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> > -------------------------------
> > Hashem Koohy
> > PhD
> > Postdoctoral Fellow,
> > Sanger Institute,
> > Cambridge
> > Mobile: 07515425433
> >
> >
> >
> >
> > --
> > ?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.
> >
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 
> End of Biojava-l Digest, Vol 105, Issue 2
> *****************************************
 		 	   		  

From xue.vin at gmail.com  Mon Oct 10 20:39:52 2011
From: xue.vin at gmail.com (Vincent Xue)
Date: Mon, 10 Oct 2011 20:39:52 -0400
Subject: [Biojava-l] Stockholm Parser Implementation?
Message-ID: <CAN9vMjktBR0ySLj0hFtGZhycO+AETLggsmJYs335bKEcjka4dQ@mail.gmail.com>

Hi,

I was wondering if there has been any work on developing a Stockholm
1.0 parser?

Thanks!

From andreas.prlic at gmail.com  Tue Oct 11 18:51:48 2011
From: andreas.prlic at gmail.com (Andreas Prlic)
Date: Tue, 11 Oct 2011 15:51:48 -0700
Subject: [Biojava-l] BioJava Help
In-Reply-To: <CA+ggGe69q1QvRHQs2xe923XrWcnKBBu9XUB91aGo4cDoLv39wA@mail.gmail.com>
References: <CA+ggGe4Efh5c8-FFFE3hS12E-4ergVcBBn2FQvT1juZTSUmpng@mail.gmail.com>
	<CALthepw8W_T0B9dSAqQOnFU1UnZjLUhqS-8dVoKd60xB9SpmCA@mail.gmail.com>
	<CA+ggGe7U1VevV+R7gyW1gFxns-zjke86F=h450z0XsRywzLtMw@mail.gmail.com>
	<CALthepyXMb9uy72cw-ORaBGnUf6LvuEHrurY+y2_4GaduvjE_A@mail.gmail.com>
	<CA+ggGe69q1QvRHQs2xe923XrWcnKBBu9XUB91aGo4cDoLv39wA@mail.gmail.com>
Message-ID: <CALthepyTq2s7U6Fm2hrStvRr=vo0LvNtu6SfZU5ERPTc4ayfVw@mail.gmail.com>

Hi Omer,

please keep such questions on the public list. Chances are high that
if you are struggling with something, somebody else is having the same
problem as well.

I wasactually talking about BioJava 1.8, the previous version of
BioJava. It is still available and the cookbook page that I meant is
here:
http://biojava.org/wiki/BioJava:CookBook:Blast:Parser

About Maven: It is probably best to start with a new project in your
favorite IDE and set it up as a Maven project that depends on BioJava.
(i.e. add the BioJava repository to the pom configuraiton). If you
think this is difficult, we can/should set up a documentation page
that explains those first steps.

Andreas



On Tue, Oct 11, 2011 at 6:34 AM, Omer Eilam <omereila at post.tau.ac.il> wrote:
> Are you referring to the BlastXMLQuery class? because I see in the API
> that it contains only one method.
> Also, I am not familiar with using Maven, I see the various biojava
> packages in the eclipse project explorer, but I don't know how to
> create a new class (i.e. do I need imports and stuff?)
>
> Thanks again!
> omer
>
> On Mon, Oct 10, 2011 at 3:58 AM, Andreas Prlic <andreas.prlic at gmail.com> wrote:
>> Hi Omer,
>>
>> Our recommendation nowadays for working with Blast is to get XML
>> output and simply parse that. Depending on what you need that will
>> give you more details than the parser that is in the BioJava 1.8
>> (legacy) project. (if you still want to give that one a try, there is
>> a cookbook page for it)
>>
>> Andreas
>>
>>
>> On Sun, Oct 9, 2011 at 2:26 AM, Omer Eilam <omereila at post.tau.ac.il> wrote:
>>> I eventually succeeded in importing Biojava.
>>> I read in the paper that there is a parser for BLAST - where can I get
>>> more information/API on this?
>>>
>>> Thanks!
>>> omer
>>>
>>> On Thu, Oct 6, 2011 at 5:35 PM, Andreas Prlic <andreas.prlic at gmail.com> wrote:
>>>> Hi Omer,
>>>>
>>>> We are having problems with the anonymous SVN server quite often. I
>>>> recommend trying the git copy at github, or their SVN interface, or
>>>> using Maven to install it.
>>>>
>>>> http://www.biojava.org/wiki/CVS_to_SVN_Migration
>>>>
>>>> Andreas
>>>>
>>>> On Thu, Oct 6, 2011 at 1:56 AM, Omer Eilam <omereila at post.tau.ac.il> wrote:
>>>>> Dear Andreas,
>>>>>
>>>>> I wish to install BioJava for my eclipse IDE.
>>>>> I followed all the instructions in the website
>>>>> http://www.biojava.org/wiki/BioJava3_eclipse.
>>>>> I currently have problems with the last step. I create a new Maven
>>>>> project, but when I try to type /biojava/biojava-live/trunk in the SCM
>>>>> URL, I get an "invalid URL" error.
>>>>> Please let me know what seems to be the problem and how can I fix it.
>>>>>
>>>>> Thanks much!
>>>>> omer
>>>>>
>>>>> --
>>>>> Omer Eilam
>>>>> Complex Network Systems
>>>>> Prof. Eytan Ruppin
>>>>> Tel-Aviv University
>>>>> http://cns.cs.tau.ac.il/
>>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> Omer Eilam
>>> Complex Network Systems
>>> Prof. Eytan Ruppin
>>> Tel-Aviv University
>>> http://cns.cs.tau.ac.il/
>>>
>>
>
>
>
> --
> Omer Eilam
> Complex Network Systems
> Prof. Eytan Ruppin
> Tel-Aviv University
> http://cns.cs.tau.ac.il/
>

From andreas.prlic at gmail.com  Wed Oct 12 12:00:14 2011
From: andreas.prlic at gmail.com (Andreas Prlic)
Date: Wed, 12 Oct 2011 09:00:14 -0700
Subject: [Biojava-l] User defined substitution matrix.
In-Reply-To: <CAEqMO2HNFfV+qtWJmp9mxP8JV_WCKu5hfCYkvi_Y3Lpf+XLafw@mail.gmail.com>
References: <CAEqMO2HNFfV+qtWJmp9mxP8JV_WCKu5hfCYkvi_Y3Lpf+XLafw@mail.gmail.com>
Message-ID: <CALthepyPiC6H=929SU2vo3BLxtF0MszzpJMjEgSP1Fyc5NPb_w@mail.gmail.com>

Hi Canan,

Please subscribe to the biojava-l mailing list for sending messages to
the list. Details for how to do that can be found here:

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

About your question:

getResourceAsStream is just opening a stream to a file that is bundled
together with a jar file. There should be no need for you to call that
to get a matrix.

If you want to use any of the (many) standard substitution matrices
that are supported by BioJava you just need to call
SubstitutionMatrixHelper .getMatrixFromAAINDEX(nameOfMatrix)

If you want to work with a matrix that is not yet the AAINDEX
collection of matrices, it depends on how the matrix is represented in
the file. If it is in the same style as in AAINDEX, you can use the
DefaultAAIndexProvider to parse your custom matrix.

Andreas




On Tue, Oct 11, 2011 at 11:09 PM, Canan Has <cananhas at iyte.edu.tr> wrote:
> Dear Dr. Prlic,
> Sorry to bother you, but my mails to biojava forum-nabble are not being
> answered. Even I have been already subscribed, I am getting alerts saying
> your message is in pending list, because you are not subscribed.?Therefore,
> I decided to ?ask my question to you directly. I hope you will answer to me.
> Because, it is so important and urgent.
> Simply,I want to create my own substitution matrix object. I examined the
> source code of SubstitutionMatrixHelper and the related others. I did some
> modifications and took null pointer exception for getResourceAsStream().
> I tried to find out where the directory for getResourceAsStream() has been
> set. At first, I thought the file directory is the resources folder in
> alignment folder. Then, I deleted one of the matrices - pam250 and tried to
> initialize it by calling getPam250() and matrix was created. This leads me
> to think that the developer introduced ftp.ncbi url to ?getResourceAsStream
> to take matrices by name.
> Can you show a way to create my own? Or you can tell me and I can change
> where the url is given and recompile the code.
> Thanks in advance
> Canan Has
> Research Assistant & MSc Student
> Computational Biology & Bioinformatics Lab
> Molecular Biology and Genetics Department
> Izmir Institute of Technology
>


From andreas at sdsc.edu  Wed Oct 12 12:05:58 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 12 Oct 2011 09:05:58 -0700
Subject: [Biojava-l] Stockholm Parser Implementation?
In-Reply-To: <CAN9vMjktBR0ySLj0hFtGZhycO+AETLggsmJYs335bKEcjka4dQ@mail.gmail.com>
References: <CAN9vMjktBR0ySLj0hFtGZhycO+AETLggsmJYs335bKEcjka4dQ@mail.gmail.com>
Message-ID: <CALthepw9K4VWQJRT1pxy+AG1UpQG345i_vQaeavkXce90GR5vw@mail.gmail.com>

Hi Vincent,

I am not aware of parser for that as part of Biojava. It would be
great to have, though. If you want to make a contribution, you would
be more than welcome ...

Andreas



On Mon, Oct 10, 2011 at 5:39 PM, Vincent Xue <xue.vin at gmail.com> wrote:
> Hi,
>
> I was wondering if there has been any work on developing a Stockholm
> 1.0 parser?
>
> Thanks!
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From jprocter at compbio.dundee.ac.uk  Fri Oct 14 05:07:01 2011
From: jprocter at compbio.dundee.ac.uk (Jim Procter)
Date: Fri, 14 Oct 2011 10:07:01 +0100
Subject: [Biojava-l] Stockholm Parser Implementation?
In-Reply-To: <CALthepw9K4VWQJRT1pxy+AG1UpQG345i_vQaeavkXce90GR5vw@mail.gmail.com>
References: <CAN9vMjktBR0ySLj0hFtGZhycO+AETLggsmJYs335bKEcjka4dQ@mail.gmail.com>
	<CALthepw9K4VWQJRT1pxy+AG1UpQG345i_vQaeavkXce90GR5vw@mail.gmail.com>
Message-ID: <4E97FBB5.5090402@compbio.dundee.ac.uk>

On 12/10/2011 17:05, Andreas Prlic wrote:
> Hi Vincent,
>
> I am not aware of parser for that as part of Biojava. It would be
> great to have, though. If you want to make a contribution, you would
> be more than welcome ...
I thought Jules worked on this - he took a look at Jalview's one and 
promptly wrote a better one, IIRC. However, whether it got in to bj3 is 
another matter!  Perhaps asking him nicely would work :)

Jim.



From kern3020 at gmail.com  Mon Oct 17 20:49:17 2011
From: kern3020 at gmail.com (John Kern)
Date: Mon, 17 Oct 2011 17:49:17 -0700
Subject: [Biojava-l] is the tutorial in sync with the latest version?
Message-ID: <CAJ-7iFV0Ac4h-zkLn_Mh5TBX+gWqFPk8+E-s6=G9UF4V4K7w5w@mail.gmail.com>

Hello,

I am not to Biojava and bioinformatics in general. I noticed your latest
release is 3.0.2 but the tutorial reference to the 1.8 release (
http://biojava.org/wiki/BioJava:Tutorial). Does this imply the tutorial is
out of sync with the tutorial?

Regards,
John

From andreas at sdsc.edu  Mon Oct 17 23:11:16 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 17 Oct 2011 20:11:16 -0700
Subject: [Biojava-l] is the tutorial in sync with the latest version?
In-Reply-To: <CAJ-7iFV0Ac4h-zkLn_Mh5TBX+gWqFPk8+E-s6=G9UF4V4K7w5w@mail.gmail.com>
References: <CAJ-7iFV0Ac4h-zkLn_Mh5TBX+gWqFPk8+E-s6=G9UF4V4K7w5w@mail.gmail.com>
Message-ID: <CALthepwyo0ZV5DpKdwTqGYL7T3789u1Zn=UovrZCDTPLMKKBMA@mail.gmail.com>

Hi John,

This Tutorial was written for what is currently the legacy 1.8
release. It would be great if somebody would volunteer and provide
such a tutorial for the current  3.X code base ...

Andreas



On Mon, Oct 17, 2011 at 5:49 PM, John Kern <kern3020 at gmail.com> wrote:
> Hello,
>
> I am not to Biojava and bioinformatics in general. I noticed your latest
> release is 3.0.2 but the tutorial reference to the 1.8 release (
> http://biojava.org/wiki/BioJava:Tutorial). Does this imply the tutorial is
> out of sync with the tutorial?
>
> Regards,
> John
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> 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
-----------------------------------------------------------------------


From biojava at hannes.oib.com  Tue Oct 18 05:46:44 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Tue, 18 Oct 2011 11:46:44 +0200
Subject: [Biojava-l] Multiple Sequence Alignment - Limits?
In-Reply-To: <CAPXi2mkLfYxixwx-Wgein7O62ojXm0w-gEdxYfOBBd1KSO-hPA@mail.gmail.com>
References: <CAPXi2mkLfYxixwx-Wgein7O62ojXm0w-gEdxYfOBBd1KSO-hPA@mail.gmail.com>
Message-ID: <CAPXi2mmErxQ7tbu8kGuszJAq7SQCqywiAyypT+mnRH7L1jZ3xA@mail.gmail.com>

On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> Hi again!
>
> I am quite happy with the Multiple Sequence Alignment, but I noticed
> that there seems to be a limit of 132 Sequences that are present in
> the final alignment - is this some kind of hardcoded limit, or can I
> work around that somehow?
>
> Hannes
>

Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
fasta format. Is there a way to work around that limit?

Hannes


From kern3020 at gmail.com  Tue Oct 18 10:42:54 2011
From: kern3020 at gmail.com (John Kern)
Date: Tue, 18 Oct 2011 07:42:54 -0700
Subject: [Biojava-l] is the tutorial in sync with the latest version?
In-Reply-To: <CALthepwyo0ZV5DpKdwTqGYL7T3789u1Zn=UovrZCDTPLMKKBMA@mail.gmail.com>
References: <CAJ-7iFV0Ac4h-zkLn_Mh5TBX+gWqFPk8+E-s6=G9UF4V4K7w5w@mail.gmail.com>
	<CALthepwyo0ZV5DpKdwTqGYL7T3789u1Zn=UovrZCDTPLMKKBMA@mail.gmail.com>
Message-ID: <CAJ-7iFVbvhsQOqSYMoCcscgN0eWpFNdupxqDQac_z8PBjvBrHw@mail.gmail.com>

Hello Andreas,

On Mon, Oct 17, 2011 at 8:11 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> It would be great if somebody would volunteer and provide
> such a tutorial for the current ?3.X code base ...

Great. Sign me up. I guess the way to proceed is to learn 3.x via the
cookbook and examples. Then return to the tutorial.

-jk


From andreas at sdsc.edu  Tue Oct 18 17:01:05 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 18 Oct 2011 14:01:05 -0700
Subject: [Biojava-l] Multiple Sequence Alignment - Limits?
In-Reply-To: <CAPXi2mmErxQ7tbu8kGuszJAq7SQCqywiAyypT+mnRH7L1jZ3xA@mail.gmail.com>
References: <CAPXi2mkLfYxixwx-Wgein7O62ojXm0w-gEdxYfOBBd1KSO-hPA@mail.gmail.com>
	<CAPXi2mmErxQ7tbu8kGuszJAq7SQCqywiAyypT+mnRH7L1jZ3xA@mail.gmail.com>
Message-ID: <CALthepz+7+KO1jo5gfiYHtJ-27jojGaHje7D55-B0sHuaZdqYw@mail.gmail.com>

Hi Hannes,

did you try to increase memory settings for your JVM?  e.g. -Xmx500M

Andreas

On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
> <biojava at hannes.oib.com> wrote:
>> Hi again!
>>
>> I am quite happy with the Multiple Sequence Alignment, but I noticed
>> that there seems to be a limit of 132 Sequences that are present in
>> the final alignment - is this some kind of hardcoded limit, or can I
>> work around that somehow?
>>
>> Hannes
>>
>
> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
> fasta format. Is there a way to work around that limit?
>
> Hannes
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From biojava at hannes.oib.com  Wed Oct 19 00:36:19 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 19 Oct 2011 06:36:19 +0200
Subject: [Biojava-l] Multiple Sequence Alignment - Limits?
In-Reply-To: <CALthepz+7+KO1jo5gfiYHtJ-27jojGaHje7D55-B0sHuaZdqYw@mail.gmail.com>
References: <CAPXi2mkLfYxixwx-Wgein7O62ojXm0w-gEdxYfOBBd1KSO-hPA@mail.gmail.com>
	<CAPXi2mmErxQ7tbu8kGuszJAq7SQCqywiAyypT+mnRH7L1jZ3xA@mail.gmail.com>
	<CALthepz+7+KO1jo5gfiYHtJ-27jojGaHje7D55-B0sHuaZdqYw@mail.gmail.com>
Message-ID: <CAPXi2mkBsBJhzfHKtgquytXPV=hF0TZNYAM8cfCcen=QfmAj+A@mail.gmail.com>

Hi Andreas,

I will try that later today if that makes any difference; I ran a
larger alignment batch overnight, and I noticed that this limit seems
to have been a coincidence; HOWEVER, the aligned sequences are always
not as many as the input sequences, is this caused by memory
constraints or how can I influence that?

Hannes

On Tue, Oct 18, 2011 at 23:01, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Hannes,
>
> did you try to increase memory settings for your JVM? ?e.g. -Xmx500M
>
> Andreas
>
> On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandst?tter-M?ller
> <biojava at hannes.oib.com> wrote:
>> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
>> <biojava at hannes.oib.com> wrote:
>>> Hi again!
>>>
>>> I am quite happy with the Multiple Sequence Alignment, but I noticed
>>> that there seems to be a limit of 132 Sequences that are present in
>>> the final alignment - is this some kind of hardcoded limit, or can I
>>> work around that somehow?
>>>
>>> Hannes
>>>
>>
>> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
>> fasta format. Is there a way to work around that limit?
>>
>> Hannes
>>
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>


From biojava at hannes.oib.com  Wed Oct 19 03:32:25 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 19 Oct 2011 09:32:25 +0200
Subject: [Biojava-l] Multiple Sequence Alignment - Limits?
In-Reply-To: <CA+P6arns8F9XeZj4UK0hEmvV_uOG5nJxoZxJ5fBQ=nDh-xuXmg@mail.gmail.com>
References: <CAPXi2mkLfYxixwx-Wgein7O62ojXm0w-gEdxYfOBBd1KSO-hPA@mail.gmail.com>
	<CAPXi2mmErxQ7tbu8kGuszJAq7SQCqywiAyypT+mnRH7L1jZ3xA@mail.gmail.com>
	<CALthepz+7+KO1jo5gfiYHtJ-27jojGaHje7D55-B0sHuaZdqYw@mail.gmail.com>
	<CAPXi2mkBsBJhzfHKtgquytXPV=hF0TZNYAM8cfCcen=QfmAj+A@mail.gmail.com>
	<CA+P6arns8F9XeZj4UK0hEmvV_uOG5nJxoZxJ5fBQ=nDh-xuXmg@mail.gmail.com>
Message-ID: <CAPXi2mnzkvLasRWixinxyh=w=V6bjePXRPhTYGF54ac5dFN57w@mail.gmail.com>

I'm currently running another test, now with even more memory for java
(500M) - it looks fine now so far. I'll re-check it later with the
other files that gave me some problems, and will report back later
today.

I had a "out of heap" exception when I tried it with the default
memory settings, and with 256M it seems to have swallowed some
sequences - I'll re-check and help you reproduce. It would be really
bad if the code would swallow sequences without error messages when
running out of memory, so I'll make sure I have proof :D

Hannes

On Wed, Oct 19, 2011 at 09:22, Spencer Bliven <sbliven at ucsd.edu> wrote:
> Hannes?
>
> There should not be a limit on the number of sequences, nor should you be
> running into a memory problem. The FastaParser should be able to read
> thousands of sequences, since it is used for genome FASTA files as well as
> multiple alignments. My guess would be either a malformed FASTA file
> (perhaps a problem with line endings?), or else a problem with the code to
> generate the MultipleAlignment. Can you post some code snippets?
>
> -Spencer
>
> On Tue, Oct 18, 2011 at 21:36, Hannes Brandst?tter-M?ller
> <biojava at hannes.oib.com> wrote:
>>
>> Hi Andreas,
>>
>> I will try that later today if that makes any difference; I ran a
>> larger alignment batch overnight, and I noticed that this limit seems
>> to have been a coincidence; HOWEVER, the aligned sequences are always
>> not as many as the input sequences, is this caused by memory
>> constraints or how can I influence that?
>>
>> Hannes
>>
>> On Tue, Oct 18, 2011 at 23:01, Andreas Prlic <andreas at sdsc.edu> wrote:
>> > Hi Hannes,
>> >
>> > did you try to increase memory settings for your JVM? ?e.g. -Xmx500M
>> >
>> > Andreas
>> >
>> > On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandst?tter-M?ller
>> > <biojava at hannes.oib.com> wrote:
>> >> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
>> >> <biojava at hannes.oib.com> wrote:
>> >>> Hi again!
>> >>>
>> >>> I am quite happy with the Multiple Sequence Alignment, but I noticed
>> >>> that there seems to be a limit of 132 Sequences that are present in
>> >>> the final alignment - is this some kind of hardcoded limit, or can I
>> >>> work around that somehow?
>> >>>
>> >>> Hannes
>> >>>
>> >>
>> >> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
>> >> fasta format. Is there a way to work around that limit?
>> >>
>> >> Hannes
>> >>
>> >> _______________________________________________
>> >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >>
>> >
>>
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>


From sbliven at ucsd.edu  Wed Oct 19 03:22:55 2011
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Wed, 19 Oct 2011 00:22:55 -0700
Subject: [Biojava-l] Multiple Sequence Alignment - Limits?
In-Reply-To: <CAPXi2mkBsBJhzfHKtgquytXPV=hF0TZNYAM8cfCcen=QfmAj+A@mail.gmail.com>
References: <CAPXi2mkLfYxixwx-Wgein7O62ojXm0w-gEdxYfOBBd1KSO-hPA@mail.gmail.com>
	<CAPXi2mmErxQ7tbu8kGuszJAq7SQCqywiAyypT+mnRH7L1jZ3xA@mail.gmail.com>
	<CALthepz+7+KO1jo5gfiYHtJ-27jojGaHje7D55-B0sHuaZdqYw@mail.gmail.com>
	<CAPXi2mkBsBJhzfHKtgquytXPV=hF0TZNYAM8cfCcen=QfmAj+A@mail.gmail.com>
Message-ID: <CA+P6arns8F9XeZj4UK0hEmvV_uOG5nJxoZxJ5fBQ=nDh-xuXmg@mail.gmail.com>

Hannes?

There should not be a limit on the number of sequences, nor should you be
running into a memory problem. The FastaParser should be able to read
thousands of sequences, since it is used for genome FASTA files as well as
multiple alignments. My guess would be either a malformed FASTA file
(perhaps a problem with line endings?), or else a problem with the code to
generate the MultipleAlignment. Can you post some code snippets?

-Spencer

On Tue, Oct 18, 2011 at 21:36, Hannes Brandst?tter-M?ller <
biojava at hannes.oib.com> wrote:

> Hi Andreas,
>
> I will try that later today if that makes any difference; I ran a
> larger alignment batch overnight, and I noticed that this limit seems
> to have been a coincidence; HOWEVER, the aligned sequences are always
> not as many as the input sequences, is this caused by memory
> constraints or how can I influence that?
>
> Hannes
>
> On Tue, Oct 18, 2011 at 23:01, Andreas Prlic <andreas at sdsc.edu> wrote:
> > Hi Hannes,
> >
> > did you try to increase memory settings for your JVM?  e.g. -Xmx500M
> >
> > Andreas
> >
> > On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandst?tter-M?ller
> > <biojava at hannes.oib.com> wrote:
> >> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
> >> <biojava at hannes.oib.com> wrote:
> >>> Hi again!
> >>>
> >>> I am quite happy with the Multiple Sequence Alignment, but I noticed
> >>> that there seems to be a limit of 132 Sequences that are present in
> >>> the final alignment - is this some kind of hardcoded limit, or can I
> >>> work around that somehow?
> >>>
> >>> Hannes
> >>>
> >>
> >> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
> >> fasta format. Is there a way to work around that limit?
> >>
> >> Hannes
> >>
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>
> >
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From jvb at Cs.Nott.AC.UK  Wed Oct 19 07:15:26 2011
From: jvb at Cs.Nott.AC.UK (jvb at Cs.Nott.AC.UK)
Date: 19 Oct 2011 12:15:26 +0100
Subject: [Biojava-l] Status of org.biojava3.data.sequence.SequenceUtil ?
Message-ID: <201110191215.aa17789@pat.Cs.Nott.AC.UK>

Hello,

I can't find a jar containing org.biojava3.data.sequence.SequenceUtil, even 
though it appears in the JavaDocs: 
http://www.biojava.org/docs/api/org/biojava3/data/sequence/SequenceUtil.html

What is it's status? Can I get it, and should it rely on it if I can?

Thanks,

Jon



From p.v.troshin at dundee.ac.uk  Wed Oct 19 11:13:44 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Wed, 19 Oct 2011 16:13:44 +0100
Subject: [Biojava-l] Status of org.biojava3.data.sequence.SequenceUtil ?
In-Reply-To: <201110191215.aa17789@pat.Cs.Nott.AC.UK>
References: <201110191215.aa17789@pat.Cs.Nott.AC.UK>
Message-ID: <4E9EE928.4050506@dundee.ac.uk>

Hi Jon,

This class is a part of protein disorder prediction JAR and a recent 
addition to BioJava. You are welcome to use if it suits your needs.
Bear in mid though that the FASTA file reader from this class reads the 
content of the whole FASTA file at once, i.e. if you are working with 
large FASTA files you will want to use something else instead. I've got 
a Stream based FASTA reader if you need one and if there is not one in 
BioJava already.
I would imagine the functionality from this class is not going to 
disappear overnight, but it may and perhaps should be merged with other 
FASTA parsers in BioJava once somebody have time to do this.

Regards,
Peter


On 19/10/2011 12:15, jvb at cs.nott.ac.uk wrote:
> Hello,
>
> I can't find a jar containing org.biojava3.data.sequence.SequenceUtil, 
> even though it appears in the JavaDocs: 
> http://www.biojava.org/docs/api/org/biojava3/data/sequence/SequenceUtil.html
>
> What is it's status? Can I get it, and should it rely on it if I can?
>
> Thanks,
>
> Jon
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From khalil.elmazouari at gmail.com  Wed Oct 19 14:36:28 2011
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Wed, 19 Oct 2011 20:36:28 +0200
Subject: [Biojava-l] Biojava-l Digest, Vol 105, Issue 12
In-Reply-To: <mailman.3.1319040003.27008.biojava-l@lists.open-bio.org>
References: <mailman.3.1319040003.27008.biojava-l@lists.open-bio.org>
Message-ID: <AA2C5AFF-E988-4EDC-8A2F-86CA67D56BDC@gmail.com>

Hi Hannes,

just did a MSA test with 521 seq... and it works. It must be a memory issue.

try something like: java -Xmx1g -jar yourApp.jar args...

If you don't have enough RAM, try with 500m as suggested by Andreas,

Regards,

Khalil



On 19 Oct 2011, at 18:00, biojava-l-request at lists.open-bio.org wrote:

> Send Biojava-l mailing list submissions to
> 	biojava-l at lists.open-bio.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://lists.open-bio.org/mailman/listinfo/biojava-l
> or, via email, send a message with subject or body 'help' to
> 	biojava-l-request at lists.open-bio.org
> 
> You can reach the person managing the list at
> 	biojava-l-owner at lists.open-bio.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Biojava-l digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: Multiple Sequence Alignment - Limits? (Andreas Prlic)
>   2. Re: Multiple Sequence Alignment - Limits?
>      (Hannes Brandst?tter-M?ller)
>   3. Re: Multiple Sequence Alignment - Limits?
>      (Hannes Brandst?tter-M?ller)
>   4. Re: Multiple Sequence Alignment - Limits? (Spencer Bliven)
>   5. Status of org.biojava3.data.sequence.SequenceUtil ?
>      (jvb at Cs.Nott.AC.UK)
>   6. Re: Status of org.biojava3.data.sequence.SequenceUtil ?
>      (Peter Troshin)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 18 Oct 2011 14:01:05 -0700
> From: Andreas Prlic <andreas at sdsc.edu>
> Subject: Re: [Biojava-l] Multiple Sequence Alignment - Limits?
> To: Hannes Brandst?tter-M?ller <biojava at hannes.oib.com>
> Cc: biojava-l <biojava-l at lists.open-bio.org>
> Message-ID:
> 	<CALthepz+7+KO1jo5gfiYHtJ-27jojGaHje7D55-B0sHuaZdqYw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Hannes,
> 
> did you try to increase memory settings for your JVM?  e.g. -Xmx500M
> 
> Andreas
> 
> On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandst?tter-M?ller
> <biojava at hannes.oib.com> wrote:
>> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
>> <biojava at hannes.oib.com> wrote:
>>> Hi again!
>>> 
>>> I am quite happy with the Multiple Sequence Alignment, but I noticed
>>> that there seems to be a limit of 132 Sequences that are present in
>>> the final alignment - is this some kind of hardcoded limit, or can I
>>> work around that somehow?
>>> 
>>> Hannes
>>> 
>> 
>> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
>> fasta format. Is there a way to work around that limit?
>> 
>> Hannes
>> 
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Wed, 19 Oct 2011 06:36:19 +0200
> From: Hannes Brandst?tter-M?ller 	<biojava at hannes.oib.com>
> Subject: Re: [Biojava-l] Multiple Sequence Alignment - Limits?
> To: Andreas Prlic <andreas at sdsc.edu>
> Cc: biojava-l <biojava-l at lists.open-bio.org>
> Message-ID:
> 	<CAPXi2mkBsBJhzfHKtgquytXPV=hF0TZNYAM8cfCcen=QfmAj+A at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Andreas,
> 
> I will try that later today if that makes any difference; I ran a
> larger alignment batch overnight, and I noticed that this limit seems
> to have been a coincidence; HOWEVER, the aligned sequences are always
> not as many as the input sequences, is this caused by memory
> constraints or how can I influence that?
> 
> Hannes
> 
> On Tue, Oct 18, 2011 at 23:01, Andreas Prlic <andreas at sdsc.edu> wrote:
>> Hi Hannes,
>> 
>> did you try to increase memory settings for your JVM? ?e.g. -Xmx500M
>> 
>> Andreas
>> 
>> On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandst?tter-M?ller
>> <biojava at hannes.oib.com> wrote:
>>> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
>>> <biojava at hannes.oib.com> wrote:
>>>> Hi again!
>>>> 
>>>> I am quite happy with the Multiple Sequence Alignment, but I noticed
>>>> that there seems to be a limit of 132 Sequences that are present in
>>>> the final alignment - is this some kind of hardcoded limit, or can I
>>>> work around that somehow?
>>>> 
>>>> Hannes
>>>> 
>>> 
>>> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
>>> fasta format. Is there a way to work around that limit?
>>> 
>>> Hannes
>>> 
>>> _______________________________________________
>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>> 
>> 
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Wed, 19 Oct 2011 09:32:25 +0200
> From: Hannes Brandst?tter-M?ller 	<biojava at hannes.oib.com>
> Subject: Re: [Biojava-l] Multiple Sequence Alignment - Limits?
> To: Spencer Bliven <sbliven at ucsd.edu>
> Cc: biojava-l <biojava-l at lists.open-bio.org>
> Message-ID:
> 	<CAPXi2mnzkvLasRWixinxyh=w=V6bjePXRPhTYGF54ac5dFN57w at mail.gmail.com>
> Content-Type: text/plain; charset=windows-1252
> 
> I'm currently running another test, now with even more memory for java
> (500M) - it looks fine now so far. I'll re-check it later with the
> other files that gave me some problems, and will report back later
> today.
> 
> I had a "out of heap" exception when I tried it with the default
> memory settings, and with 256M it seems to have swallowed some
> sequences - I'll re-check and help you reproduce. It would be really
> bad if the code would swallow sequences without error messages when
> running out of memory, so I'll make sure I have proof :D
> 
> Hannes
> 
> On Wed, Oct 19, 2011 at 09:22, Spencer Bliven <sbliven at ucsd.edu> wrote:
>> Hannes?
>> 
>> There should not be a limit on the number of sequences, nor should you be
>> running into a memory problem. The FastaParser should be able to read
>> thousands of sequences, since it is used for genome FASTA files as well as
>> multiple alignments. My guess would be either a malformed FASTA file
>> (perhaps a problem with line endings?), or else a problem with the code to
>> generate the MultipleAlignment. Can you post some code snippets?
>> 
>> -Spencer
>> 
>> On Tue, Oct 18, 2011 at 21:36, Hannes Brandst?tter-M?ller
>> <biojava at hannes.oib.com> wrote:
>>> 
>>> Hi Andreas,
>>> 
>>> I will try that later today if that makes any difference; I ran a
>>> larger alignment batch overnight, and I noticed that this limit seems
>>> to have been a coincidence; HOWEVER, the aligned sequences are always
>>> not as many as the input sequences, is this caused by memory
>>> constraints or how can I influence that?
>>> 
>>> Hannes
>>> 
>>> On Tue, Oct 18, 2011 at 23:01, Andreas Prlic <andreas at sdsc.edu> wrote:
>>>> Hi Hannes,
>>>> 
>>>> did you try to increase memory settings for your JVM? ?e.g. -Xmx500M
>>>> 
>>>> Andreas
>>>> 
>>>> On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandst?tter-M?ller
>>>> <biojava at hannes.oib.com> wrote:
>>>>> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
>>>>> <biojava at hannes.oib.com> wrote:
>>>>>> Hi again!
>>>>>> 
>>>>>> I am quite happy with the Multiple Sequence Alignment, but I noticed
>>>>>> that there seems to be a limit of 132 Sequences that are present in
>>>>>> the final alignment - is this some kind of hardcoded limit, or can I
>>>>>> work around that somehow?
>>>>>> 
>>>>>> Hannes
>>>>>> 
>>>>> 
>>>>> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
>>>>> fasta format. Is there a way to work around that limit?
>>>>> 
>>>>> Hannes
>>>>> 
>>>>> _______________________________________________
>>>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>> 
>>>> 
>>> 
>>> _______________________________________________
>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
>> 
> 
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Wed, 19 Oct 2011 00:22:55 -0700
> From: Spencer Bliven <sbliven at ucsd.edu>
> Subject: Re: [Biojava-l] Multiple Sequence Alignment - Limits?
> To: Hannes Brandst?tter-M?ller <biojava at hannes.oib.com>
> Cc: biojava-l <biojava-l at lists.open-bio.org>
> Message-ID:
> 	<CA+P6arns8F9XeZj4UK0hEmvV_uOG5nJxoZxJ5fBQ=nDh-xuXmg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> Hannes?
> 
> There should not be a limit on the number of sequences, nor should you be
> running into a memory problem. The FastaParser should be able to read
> thousands of sequences, since it is used for genome FASTA files as well as
> multiple alignments. My guess would be either a malformed FASTA file
> (perhaps a problem with line endings?), or else a problem with the code to
> generate the MultipleAlignment. Can you post some code snippets?
> 
> -Spencer
> 
> On Tue, Oct 18, 2011 at 21:36, Hannes Brandst?tter-M?ller <
> biojava at hannes.oib.com> wrote:
> 
>> Hi Andreas,
>> 
>> I will try that later today if that makes any difference; I ran a
>> larger alignment batch overnight, and I noticed that this limit seems
>> to have been a coincidence; HOWEVER, the aligned sequences are always
>> not as many as the input sequences, is this caused by memory
>> constraints or how can I influence that?
>> 
>> Hannes
>> 
>> On Tue, Oct 18, 2011 at 23:01, Andreas Prlic <andreas at sdsc.edu> wrote:
>>> Hi Hannes,
>>> 
>>> did you try to increase memory settings for your JVM?  e.g. -Xmx500M
>>> 
>>> Andreas
>>> 
>>> On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandst?tter-M?ller
>>> <biojava at hannes.oib.com> wrote:
>>>> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
>>>> <biojava at hannes.oib.com> wrote:
>>>>> Hi again!
>>>>> 
>>>>> I am quite happy with the Multiple Sequence Alignment, but I noticed
>>>>> that there seems to be a limit of 132 Sequences that are present in
>>>>> the final alignment - is this some kind of hardcoded limit, or can I
>>>>> work around that somehow?
>>>>> 
>>>>> Hannes
>>>>> 
>>>> 
>>>> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
>>>> fasta format. Is there a way to work around that limit?
>>>> 
>>>> Hannes
>>>> 
>>>> _______________________________________________
>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>> 
>>> 
>> 
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
> 
> 
> 
> ------------------------------
> 
> Message: 5
> Date: 19 Oct 2011 12:15:26 +0100
> From: jvb at Cs.Nott.AC.UK
> Subject: [Biojava-l] Status of org.biojava3.data.sequence.SequenceUtil
> 	?
> To: biojava-l <biojava-l at lists.open-bio.org>
> Message-ID: <201110191215.aa17789 at pat.Cs.Nott.AC.UK>
> Content-Type: text/plain; format=flowed; charset=ISO-8859-1
> 
> Hello,
> 
> I can't find a jar containing org.biojava3.data.sequence.SequenceUtil, even 
> though it appears in the JavaDocs: 
> http://www.biojava.org/docs/api/org/biojava3/data/sequence/SequenceUtil.html
> 
> What is it's status? Can I get it, and should it rely on it if I can?
> 
> Thanks,
> 
> Jon
> 
> 
> 
> 
> ------------------------------
> 
> Message: 6
> Date: Wed, 19 Oct 2011 16:13:44 +0100
> From: Peter Troshin <p.v.troshin at dundee.ac.uk>
> Subject: Re: [Biojava-l] Status of
> 	org.biojava3.data.sequence.SequenceUtil ?
> To: jvb at cs.nott.ac.uk
> Cc: biojava-l at lists.open-bio.org
> Message-ID: <4E9EE928.4050506 at dundee.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi Jon,
> 
> This class is a part of protein disorder prediction JAR and a recent 
> addition to BioJava. You are welcome to use if it suits your needs.
> Bear in mid though that the FASTA file reader from this class reads the 
> content of the whole FASTA file at once, i.e. if you are working with 
> large FASTA files you will want to use something else instead. I've got 
> a Stream based FASTA reader if you need one and if there is not one in 
> BioJava already.
> I would imagine the functionality from this class is not going to 
> disappear overnight, but it may and perhaps should be merged with other 
> FASTA parsers in BioJava once somebody have time to do this.
> 
> Regards,
> Peter
> 
> 
> On 19/10/2011 12:15, jvb at cs.nott.ac.uk wrote:
>> Hello,
>> 
>> I can't find a jar containing org.biojava3.data.sequence.SequenceUtil, 
>> even though it appears in the JavaDocs: 
>> http://www.biojava.org/docs/api/org/biojava3/data/sequence/SequenceUtil.html
>> 
>> What is it's status? Can I get it, and should it rely on it if I can?
>> 
>> Thanks,
>> 
>> Jon
>> 
>> 
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 
> End of Biojava-l Digest, Vol 105, Issue 12
> ******************************************



From biojava at hannes.oib.com  Thu Oct 20 08:29:14 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 20 Oct 2011 14:29:14 +0200
Subject: [Biojava-l] Undeclared/uncaught exception in Fasta Parser
Message-ID: <CAPXi2mngKukzTPS+2PDcUiEY3N3hULuz91BpMtgdOzuRcCgVOQ@mail.gmail.com>

If you feed the fasta parser (code from cookbook) with an empty file, you get a
java.lang.ArrayIndexOutOfBoundsException: 0
        at org.biojava3.core.sequence.io.GenericFastaHeaderParser.parseHeader(GenericFastaHeaderParser.java:111)
        at org.biojava3.core.sequence.io.GenericFastaHeaderParser.parseHeader(GenericFastaHeaderParser.java:60)
        at org.biojava3.core.sequence.io.FastaReader.process(FastaReader.java:136)


Code:

FileInputStream inStream = new FileInputStream(inputFileName);
       FastaReader<DNASequence, NucleotideCompound> fastaReader =
               new FastaReader<DNASequence, NucleotideCompound>(
               inStream,
               new GenericFastaHeaderParser<DNASequence, NucleotideCompound>(),
               new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
       LinkedHashMap<String, DNASequence> originalSeqs =
fastaReader.process(); //boom!

I believe this exception should either be caught and converted to an
IOException or declared.

Hannes

ps: I also ran into an OutOfMemoryError, I tried MSA with approx.
1000+ sequences :D even though I gave java 4000M - are there any
metrics I can use before starting the MSA to determine If it can work?

java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError:
GC overhead limit exceeded
        at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:252)
        at java.util.concurrent.FutureTask.get(FutureTask.java:111)
        at org.biojava3.alignment.Alignments.getProgressiveAlignment(Alignments.java:560)
        at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:187)
        at ...
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
        at java.lang.Integer.valueOf(Integer.java:601)
        at org.biojava3.core.sequence.location.SimplePoint.getPosition(SimplePoint.java:55)
        at org.biojava3.alignment.SimpleAlignedSequence.isGap(SimpleAlignedSequence.java:231)
        at org.biojava3.alignment.SimpleAlignedSequence.getSequenceIndexAt(SimpleAlignedSequence.java:205)
        at org.biojava3.alignment.SimpleAlignedSequence.getCompoundAt(SimpleAlignedSequence.java:270)
        at org.biojava3.alignment.SimpleProfile.getCompoundsAt(SimpleProfile.java:231)
        at org.biojava3.alignment.SimpleProfile.getCompoundCountsAt(SimpleProfile.java:217)
        at org.biojava3.alignment.SimpleProfile.getCompoundWeightsAt(SimpleProfile.java:249)
        at org.biojava3.alignment.template.AbstractProfileProfileAligner.reset(AbstractProfileProfileAligner.java:235)
        at org.biojava3.alignment.template.AbstractProfileProfileAligner.isReady(AbstractProfileProfileAligner.java:215)
        at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:270)
        at org.biojava3.alignment.template.AbstractProfileProfileAligner.getPair(AbstractProfileProfileAligner.java:158)
        at org.biojava3.alignment.template.CallableProfileProfileAligner.call(CallableProfileProfileAligner.java:54)
        at org.biojava3.alignment.template.CallableProfileProfileAligner.call(CallableProfileProfileAligner.java:38)
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
        at java.util.concurrent.FutureTask.run(FutureTask.java:166)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
        at java.lang.Thread.run(Thread.java:636)
java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError:
GC overhead limit exceeded
        at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:252)
        at java.util.concurrent.FutureTask.get(FutureTask.java:111)
        at org.biojava3.alignment.template.AbstractProfileProfileAligner.isReady(AbstractProfileProfileAligner.java:210)
        at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:270)
        at org.biojava3.alignment.template.AbstractProfileProfileAligner.getPair(AbstractProfileProfileAligner.java:158)
        at org.biojava3.alignment.template.CallableProfileProfileAligner.call(CallableProfileProfileAligner.java:54)
        at org.biojava3.alignment.template.CallableProfileProfileAligner.call(CallableProfileProfileAligner.java:38)
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
        at java.util.concurrent.FutureTask.run(FutureTask.java:166)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
        at java.lang.Thread.run(Thread.java:636)
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
        at java.lang.Integer.valueOf(Integer.java:601)
        at org.biojava3.core.sequence.location.SimplePoint.getPosition(SimplePoint.java:55)
        at org.biojava3.alignment.SimpleAlignedSequence.isGap(SimpleAlignedSequence.java:231)
        at org.biojava3.alignment.SimpleAlignedSequence.getSequenceIndexAt(SimpleAlignedSequence.java:205)
        at org.biojava3.alignment.SimpleAlignedSequence.getCompoundAt(SimpleAlignedSequence.java:270)
        at org.biojava3.alignment.SimpleProfile.getCompoundsAt(SimpleProfile.java:231)
        at org.biojava3.alignment.SimpleProfile.getCompoundCountsAt(SimpleProfile.java:217)
        at org.biojava3.alignment.SimpleProfile.getCompoundWeightsAt(SimpleProfile.java:249)
        at org.biojava3.alignment.template.AbstractProfileProfileAligner.reset(AbstractProfileProfileAligner.java:235)
        at org.biojava3.alignment.template.AbstractProfileProfileAligner.isReady(AbstractProfileProfileAligner.java:215)
        ... 9 more

From kern3020 at gmail.com  Thu Oct 20 12:19:27 2011
From: kern3020 at gmail.com (John Kern)
Date: Thu, 20 Oct 2011 09:19:27 -0700
Subject: [Biojava-l]  Multiple Sequence Alignment - Limits?
Message-ID: <CAJ-7iFW=qzwwKLHuzkhp13g0nup4iNsnZTZa9rM6GOVC3Pk_qw@mail.gmail.com>

Hello Hannes,

When programs run out of memory it can be insightful to look at them
via the operating system. It helps to determine if the program
consumes all the memory or is hitting another limit. These comments
are specific to Lunix. All versions of UNIX have similar shells. If
you are running Windows, this is not relevant.

Process size can be limited by a shell on unix systems.

$ man sh
$ ulimit -a
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 20
file size               (blocks, -f) unlimited
pending signals                 (-i) 16382
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) unlimited
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

On my system, there are now limits. What are the results on your system?

If the shell is not limiting your process and as other have pointed
out the JVM isn't limited, the program top can be very insightful.
http://www.kernelhardware.org/linux-top-command/

When the program is running out of memory, does top confirm you have
no more memory?

Regards,
John

From kern3020 at gmail.com  Thu Oct 20 16:12:39 2011
From: kern3020 at gmail.com (John Kern)
Date: Thu, 20 Oct 2011 13:12:39 -0700
Subject: [Biojava-l] demos from 1.8
Message-ID: <CAJ-7iFXugc7rX=4Nc9daufCOh7Y-PxGppnuB8DQAdefNJrLvpw@mail.gmail.com>

Hello,

The 1.8 tutorial refers to a demos directory.
"Additionally, a number of small demo programs can be found in the
demos directory of the BioJava source distribution."

Would it make sense to migrate them to the 3.x APIs?

I downloaded the aggregate tar ball for 1.8.1.  I do not see it there.
Where can I find it?

Thanks,
-john

From andreas at sdsc.edu  Thu Oct 20 17:19:27 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 20 Oct 2011 14:19:27 -0700
Subject: [Biojava-l] demos from 1.8
In-Reply-To: <CAJ-7iFXugc7rX=4Nc9daufCOh7Y-PxGppnuB8DQAdefNJrLvpw@mail.gmail.com>
References: <CAJ-7iFXugc7rX=4Nc9daufCOh7Y-PxGppnuB8DQAdefNJrLvpw@mail.gmail.com>
Message-ID: <CALthepzB89x3twD+-xTQBBaPSbSzzHvY7zvOH0LH6w_BtHdO-A@mail.gmail.com>

Hi John,

several of the 3.X modules have a demo directory that give examples
how to work with them. I believe in the old code base there was also a
demo directory somewhere, not sure if it gets bundled in the aggregate
tar ball though.

Andreas


On Thu, Oct 20, 2011 at 1:12 PM, John Kern <kern3020 at gmail.com> wrote:
> Hello,
>
> The 1.8 tutorial refers to a demos directory.
> "Additionally, a number of small demo programs can be found in the
> demos directory of the BioJava source distribution."
>
> Would it make sense to migrate them to the 3.x APIs?
>
> I downloaded the aggregate tar ball for 1.8.1. ?I do not see it there.
> Where can I find it?
>
> Thanks,
> -john
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From kern3020 at gmail.com  Thu Oct 20 17:33:56 2011
From: kern3020 at gmail.com (John Kern)
Date: Thu, 20 Oct 2011 14:33:56 -0700
Subject: [Biojava-l] demos from 1.8
In-Reply-To: <CALthepzB89x3twD+-xTQBBaPSbSzzHvY7zvOH0LH6w_BtHdO-A@mail.gmail.com>
References: <CAJ-7iFXugc7rX=4Nc9daufCOh7Y-PxGppnuB8DQAdefNJrLvpw@mail.gmail.com>
	<CALthepzB89x3twD+-xTQBBaPSbSzzHvY7zvOH0LH6w_BtHdO-A@mail.gmail.com>
Message-ID: <CAJ-7iFXAK7OxmAyhq5U5qNaaS5UxEak8vuLgUD2Z14RAdFDt1g@mail.gmail.com>

Hello Andreas,

I checked out the 3.x branch from subversion. I see two demo directories.

jkern at ubuntu:~/src/java/biojava-trunk/biojava/biojava3-core/src/main/java/org/biojava3/core/sequence$
find ~/src/java/biojava-trunk/ -name demo
/home/jkern/src/java/biojava-trunk/biojava/biojava3-structure-gui/src/main/java/demo
/home/jkern/src/java/biojava-trunk/biojava/biojava3-structure/src/main/java/demo

I found no corresponding directories in the 1.8.1 tar ball.

One of the articles
(http://biojava.org/wiki/BioJava:Tutorial:Dynamic_programming_examples)
refers to a source file called Dice.java. Would it make sense to
migrate it to the new source? If so, do you know where I can find it?

-jk


On Thu, Oct 20, 2011 at 2:19 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi John,
>
> several of the 3.X modules have a demo directory that give examples
> how to work with them. I believe in the old code base there was also a
> demo directory somewhere, not sure if it gets bundled in the aggregate
> tar ball though.
>
> Andreas
>
>
> On Thu, Oct 20, 2011 at 1:12 PM, John Kern <kern3020 at gmail.com> wrote:
>> Hello,
>>
>> The 1.8 tutorial refers to a demos directory.
>> "Additionally, a number of small demo programs can be found in the
>> demos directory of the BioJava source distribution."
>>
>> Would it make sense to migrate them to the 3.x APIs?
>>
>> I downloaded the aggregate tar ball for 1.8.1. ?I do not see it there.
>> Where can I find it?
>>
>> Thanks,
>> -john
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>


From andreas at sdsc.edu  Thu Oct 20 17:37:44 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 20 Oct 2011 14:37:44 -0700
Subject: [Biojava-l] demos from 1.8
In-Reply-To: <CAJ-7iFXAK7OxmAyhq5U5qNaaS5UxEak8vuLgUD2Z14RAdFDt1g@mail.gmail.com>
References: <CAJ-7iFXugc7rX=4Nc9daufCOh7Y-PxGppnuB8DQAdefNJrLvpw@mail.gmail.com>
	<CALthepzB89x3twD+-xTQBBaPSbSzzHvY7zvOH0LH6w_BtHdO-A@mail.gmail.com>
	<CAJ-7iFXAK7OxmAyhq5U5qNaaS5UxEak8vuLgUD2Z14RAdFDt1g@mail.gmail.com>
Message-ID: <CALthepzEXkb8agfueon_xcUUgq+dYd6PPm-YQfd5NF7M0wNnNw@mail.gmail.com>

I think that most of those demos are heavily dependent on 1.8 code and
would need some major refactoring to work for 3.x. The best reference
to get started is the Cookbook ... (and we probably need more examples
there for 3.X )

Andreas

On Thu, Oct 20, 2011 at 2:33 PM, John Kern <kern3020 at gmail.com> wrote:
> Hello Andreas,
>
> I checked out the 3.x branch from subversion. I see two demo directories.
>
> jkern at ubuntu:~/src/java/biojava-trunk/biojava/biojava3-core/src/main/java/org/biojava3/core/sequence$
> find ~/src/java/biojava-trunk/ -name demo
> /home/jkern/src/java/biojava-trunk/biojava/biojava3-structure-gui/src/main/java/demo
> /home/jkern/src/java/biojava-trunk/biojava/biojava3-structure/src/main/java/demo
>
> I found no corresponding directories in the 1.8.1 tar ball.
>
> One of the articles
> (http://biojava.org/wiki/BioJava:Tutorial:Dynamic_programming_examples)
> refers to a source file called Dice.java. Would it make sense to
> migrate it to the new source? If so, do you know where I can find it?
>
> -jk
>
>
> On Thu, Oct 20, 2011 at 2:19 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> Hi John,
>>
>> several of the 3.X modules have a demo directory that give examples
>> how to work with them. I believe in the old code base there was also a
>> demo directory somewhere, not sure if it gets bundled in the aggregate
>> tar ball though.
>>
>> Andreas
>>
>>
>> On Thu, Oct 20, 2011 at 1:12 PM, John Kern <kern3020 at gmail.com> wrote:
>>> Hello,
>>>
>>> The 1.8 tutorial refers to a demos directory.
>>> "Additionally, a number of small demo programs can be found in the
>>> demos directory of the BioJava source distribution."
>>>
>>> Would it make sense to migrate them to the 3.x APIs?
>>>
>>> I downloaded the aggregate tar ball for 1.8.1. ?I do not see it there.
>>> Where can I find it?
>>>
>>> Thanks,
>>> -john
>>> _______________________________________________
>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>
>


From kern3020 at gmail.com  Tue Oct 25 20:55:39 2011
From: kern3020 at gmail.com (John Kern)
Date: Tue, 25 Oct 2011 17:55:39 -0700
Subject: [Biojava-l] demo directory in API
Message-ID: <CAJ-7iFXjp_HGyz=HQ05igt+xwi__Ld++HUC9d-s54tSjdmkwdg@mail.gmail.com>

Hello,

While reviewing the BioJava 3.x API
(http://www.biojava.org/docs/api/index.html), I noticed the demo
directory Andreas mentioned. I do see it in neither 3.0.2 tarball nor
the subversion checkout from the trunk. If there is a demo directory
for the current source base, I would love to see it.

-jk

From andreas at sdsc.edu  Tue Oct 25 21:00:44 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 25 Oct 2011 18:00:44 -0700
Subject: [Biojava-l] demo directory in API
In-Reply-To: <CAJ-7iFXjp_HGyz=HQ05igt+xwi__Ld++HUC9d-s54tSjdmkwdg@mail.gmail.com>
References: <CAJ-7iFXjp_HGyz=HQ05igt+xwi__Ld++HUC9d-s54tSjdmkwdg@mail.gmail.com>
Message-ID: <CALthepz_rOLmVcXui86aMgsrYO1LC0VDwSQ7r7jSor4pDVerNQ@mail.gmail.com>

it is in the structure module.

Andreas

On Tue, Oct 25, 2011 at 5:55 PM, John Kern <kern3020 at gmail.com> wrote:
> Hello,
>
> While reviewing the BioJava 3.x API
> (http://www.biojava.org/docs/api/index.html), I noticed the demo
> directory Andreas mentioned. I do see it in neither 3.0.2 tarball nor
> the subversion checkout from the trunk. If there is a demo directory
> for the current source base, I would love to see it.
>
> -jk
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From kern3020 at gmail.com  Wed Oct 26 19:00:46 2011
From: kern3020 at gmail.com (John Kern)
Date: Wed, 26 Oct 2011 16:00:46 -0700
Subject: [Biojava-l] What's a good sequence to highlight features in BioJava?
Message-ID: <CAJ-7iFXnoo_LBnPGU3panVJfQz2D=k3WXcHYteXdd8HLJk6OLA@mail.gmail.com>

Hello,

Based I reviewing the 1.8 version of the tutorial, I want to write a
section in the tutorial about features, locations and annotations.
Would someone recommend a good sequence(s) to work with?

Thanks,
-John

From andreas at sdsc.edu  Thu Oct 27 13:44:03 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 27 Oct 2011 10:44:03 -0700
Subject: [Biojava-l] What's a good sequence to highlight features in
	BioJava?
In-Reply-To: <CAJ-7iFXnoo_LBnPGU3panVJfQz2D=k3WXcHYteXdd8HLJk6OLA@mail.gmail.com>
References: <CAJ-7iFXnoo_LBnPGU3panVJfQz2D=k3WXcHYteXdd8HLJk6OLA@mail.gmail.com>
Message-ID: <CALthepzhsVH8JO6q9Wn=fyPxvqhAwFmvjmrf2k4QQg8-+3Eo6w@mail.gmail.com>

Hi John,

Are you working on the 1.8 tutorial? It would be better to focus
documentation efforts on the 3.X branch! We declared the 1.8 code base
to be legacy and all developmental efforts are happening on the 3.X
trunk.

Andreas


On Wed, Oct 26, 2011 at 4:00 PM, John Kern <kern3020 at gmail.com> wrote:
> Hello,
>
> Based I reviewing the 1.8 version of the tutorial, I want to write a
> section in the tutorial about features, locations and annotations.
> Would someone recommend a good sequence(s) to work with?
>
> Thanks,
> -John
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From kern3020 at gmail.com  Thu Oct 27 15:20:54 2011
From: kern3020 at gmail.com (John Kern)
Date: Thu, 27 Oct 2011 12:20:54 -0700
Subject: [Biojava-l] What's a good sequence to highlight features in
	BioJava?
In-Reply-To: <CALthepzhsVH8JO6q9Wn=fyPxvqhAwFmvjmrf2k4QQg8-+3Eo6w@mail.gmail.com>
References: <CAJ-7iFXnoo_LBnPGU3panVJfQz2D=k3WXcHYteXdd8HLJk6OLA@mail.gmail.com>
	<CALthepzhsVH8JO6q9Wn=fyPxvqhAwFmvjmrf2k4QQg8-+3Eo6w@mail.gmail.com>
Message-ID: <CAJ-7iFVLcGEHhD6aygzvUe26zdx-w7a3mK=aGJDxUp3FLb1hEw@mail.gmail.com>

Hello Andreas,

I was still looking at it at a very high level. I want to understand
the appropriate workflow for BioJava. I am a software engineer. I do
not share your background in biology but I want to learn as much as I
possible. I am reading a college-level introduction to biology.
Additional suggestions to my read list would be appreciated.

On Thu, Oct 27, 2011 at 10:44 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Are you working on the 1.8 tutorial? It would be better to focus
> documentation efforts on the 3.X branch! We declared the 1.8 code base
> to be legacy and all developmental efforts are happening on the 3.X
> trunk.

Thanks. I will do that.

Sincerely,
John

From tiagoantao at gmail.com  Mon Oct  3 22:12:18 2011
From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=)
Date: Mon, 3 Oct 2011 23:12:18 +0100
Subject: [Biojava-l] VCF parser
Message-ID: <CAA9RGEOdgq9=Y5oruhjycP8Jw545rwDQG_eXKFzWKXYj2s3uQQ@mail.gmail.com>

Hi,

I wonder if there is a VCF parser in either Python or Java? Either I
am being dumb at searching (probably) or nothing exists?

Thanks,
Tiago

-- 
"If you want to get laid, go to college.? If you want an education, go
to the library." - Frank Zappa



From biojava at hannes.oib.com  Wed Oct  5 07:41:57 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 5 Oct 2011 09:41:57 +0200
Subject: [Biojava-l] NullPointerException when using
	Alignments.getMultipleSequenceAlignment
Message-ID: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com>

Hello!

I tried to follow http://biojava.org/wiki/BioJava:CookBook3:MSA, but
when I run it, I get:

java.util.concurrent.ExecutionException: java.lang.NullPointerException
	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
	at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
	at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
	at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173)

 What could I be doing wrong?

(
on the cookbook page, there is also an import missing:
import org.biojava3.alignment.Alignments;
)
-> then the cookbook runs, but my code does not

private static void processFile(String filename) {
        try {
            FileInputStream inStream = new FileInputStream(filename);
            FastaReader<DNASequence, NucleotideCompound> fastaReader =
                    new FastaReader<DNASequence, NucleotideCompound>(
                    inStream,
                    new GenericFastaHeaderParser<DNASequence,
NucleotideCompound>(),
                    new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
            LinkedHashMap<String, DNASequence> b = fastaReader.process();

            List<DNASequence> sequences = new ArrayList<DNASequence>();
            for (Entry<String, DNASequence> entry : b.entrySet()) {
                if (sequences.size() < 5) {
                    sequences.add(entry.getValue());
                }
                System.out.println(entry.getValue());
            }

            Profile<DNASequence, NucleotideCompound> profile =
Alignments.getMultipleSequenceAlignment(sequences);
            System.out.printf("Clustalw:%n%s%n", profile);

            ConcurrencyTools.shutdown();
        } catch (Exception ex) {
            Logger.getLogger(App.class.getName()).log(Level.SEVERE, null, ex);
        }
    }


From biojava at hannes.oib.com  Wed Oct  5 08:50:33 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 5 Oct 2011 10:50:33 +0200
Subject: [Biojava-l] NullPointerException when using
	Alignments.getMultipleSequenceAlignment
In-Reply-To: <CAB1D7DF.1E3D%hk3@sanger.ac.uk>
References: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com>
	<CAB1D7DF.1E3D%hk3@sanger.ac.uk>
Message-ID: <CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com>

Hi!

I read the sequence from a fasta file.

FileInputStream inStream = new FileInputStream(filename);
            FastaReader<DNASequence, NucleotideCompound> fastaReader =
                    new FastaReader<DNASequence, NucleotideCompound>(
                    inStream,
                    new GenericFastaHeaderParser<DNASequence,
NucleotideCompound>(),
                    new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
            LinkedHashMap<String, DNASequence> b = fastaReader.process();

and then use
List<DNASequence> sequences = new ArrayList<DNASequence>();
            for (Entry<String, DNASequence> entry : b.entrySet()) {
                sequences.add(entry.getValue());
}

to get the required list of DNA sequences.

I noticed in an earlier discussion, there was some talk about this too
(3-4 months ago, perhaps) and something about a possible fix in SVN.
when will it be released on the maven server?

Hannes

On Wed, Oct 5, 2011 at 10:46, Hashem Koohy <hk3 at sanger.ac.uk> wrote:
> Hi Hannes,
> It seems to me it doesn't like your ?dna Sequence!
> Is your sequence in the following format?
>
> Sequence dnaSeq = DNATools.createDNASequence("acccgggttttacagt", "id");
>
> Good luck
> Hashem
>
> On 05/10/2011 08:41, "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com>
> wrote:
>
>> Hello!
>>
>> I tried to follow http://biojava.org/wiki/BioJava:CookBook3:MSA, but
>> when I run it, I get:
>>
>> java.util.concurrent.ExecutionException: java.lang.NullPointerException
>> at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
>> at java.util.concurrent.FutureTask.get(FutureTask.java:83)
>> at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
>> at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
>> at
>> org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java
>> :173)
>>
>> ?What could I be doing wrong?
>>
>> (
>> on the cookbook page, there is also an import missing:
>> import org.biojava3.alignment.Alignments;
>> )
>> -> then the cookbook runs, but my code does not
>>
>> private static void processFile(String filename) {
>> ? ? ? ? try {
>> ? ? ? ? ? ? FileInputStream inStream = new FileInputStream(filename);
>> ? ? ? ? ? ? FastaReader<DNASequence, NucleotideCompound> fastaReader =
>> ? ? ? ? ? ? ? ? ? ? new FastaReader<DNASequence, NucleotideCompound>(
>> ? ? ? ? ? ? ? ? ? ? inStream,
>> ? ? ? ? ? ? ? ? ? ? new GenericFastaHeaderParser<DNASequence,
>> NucleotideCompound>(),
>> ? ? ? ? ? ? ? ? ? ? new
>> DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
>> ? ? ? ? ? ? LinkedHashMap<String, DNASequence> b = fastaReader.process();
>>
>> ? ? ? ? ? ? List<DNASequence> sequences = new ArrayList<DNASequence>();
>> ? ? ? ? ? ? for (Entry<String, DNASequence> entry : b.entrySet()) {
>> ? ? ? ? ? ? ? ? if (sequences.size() < 5) {
>> ? ? ? ? ? ? ? ? ? ? sequences.add(entry.getValue());
>> ? ? ? ? ? ? ? ? }
>> ? ? ? ? ? ? ? ? System.out.println(entry.getValue());
>> ? ? ? ? ? ? }
>>
>> ? ? ? ? ? ? Profile<DNASequence, NucleotideCompound> profile =
>> Alignments.getMultipleSequenceAlignment(sequences);
>> ? ? ? ? ? ? System.out.printf("Clustalw:%n%s%n", profile);
>>
>> ? ? ? ? ? ? ConcurrencyTools.shutdown();
>> ? ? ? ? } catch (Exception ex) {
>> ? ? ? ? ? ? Logger.getLogger(App.class.getName()).log(Level.SEVERE, null, ex);
>> ? ? ? ? }
>> ? ? }
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> -------------------------------
> Hashem Koohy
> PhD
> Postdoctoral Fellow,
> Sanger Institute,
> Cambridge
> Mobile: 07515425433
>
>
>
>
> --
> ?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.
>



From andreas at sdsc.edu  Wed Oct  5 17:21:19 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 5 Oct 2011 10:21:19 -0700
Subject: [Biojava-l] NullPointerException when using
	Alignments.getMultipleSequenceAlignment
In-Reply-To: <CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com>
References: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com>
	<CAB1D7DF.1E3D%hk3@sanger.ac.uk>
	<CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com>
Message-ID: <CALthepzPycvfecN9Ln8fvL6Q3PYR0HEbqfAfD9Ysa770E3dsJQ@mail.gmail.com>

Hi Hannes,

> I noticed in an earlier discussion, there was some talk about this too
> (3-4 months ago, perhaps) and something about a possible fix in SVN.
> when will it be released on the maven server?

What version are you on? We released Maven 3.0.2 just recently..

Andreas


From sbliven at ucsd.edu  Wed Oct  5 17:39:42 2011
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Wed, 5 Oct 2011 10:39:42 -0700
Subject: [Biojava-l] NullPointerException when using
	Alignments.getMultipleSequenceAlignment
In-Reply-To: <CALthepzPycvfecN9Ln8fvL6Q3PYR0HEbqfAfD9Ysa770E3dsJQ@mail.gmail.com>
References: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com>
	<CAB1D7DF.1E3D%hk3@sanger.ac.uk>
	<CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com>
	<CALthepzPycvfecN9Ln8fvL6Q3PYR0HEbqfAfD9Ysa770E3dsJQ@mail.gmail.com>
Message-ID: <CA+P6arkm11zAB3du8JVKxcEGh-5XXqFKMpsVa8W6w6qxAVcSLA@mail.gmail.com>

In the current SVN code (and therefor probably Biojava 3.0.2),
CookbookMSA.java includes that import statement but is otherwise identical
to the wiki version. It runs just fine for me. Probably updating to Biojava
3.0.2 will fix the null pointer exception.

This does highlight the problem of keeping the wiki synchronized with the
current BioJava version. Ideally, part of the release process could include
automated updating of the wiki cookbook from the SVN code, with older
versions available as a reference. However, I'm not sure that anyone would
be willing to set up such a complex release process.

-Spencer

On Wed, Oct 5, 2011 at 10:21, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi Hannes,
>
> > I noticed in an earlier discussion, there was some talk about this too
> > (3-4 months ago, perhaps) and something about a possible fix in SVN.
> > when will it be released on the maven server?
>
> What version are you on? We released Maven 3.0.2 just recently..
>
> Andreas
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From amr_alhossary at hotmail.com  Wed Oct  5 18:26:16 2011
From: amr_alhossary at hotmail.com (Amr AL-Hossary)
Date: Wed, 5 Oct 2011 20:26:16 +0200
Subject: [Biojava-l] NullPointerException when
	usingAlignments.getMultipleSequenceAlignment
In-Reply-To: <CA+P6arkm11zAB3du8JVKxcEGh-5XXqFKMpsVa8W6w6qxAVcSLA@mail.gmail.com>
References: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com><CAB1D7DF.1E3D%hk3@sanger.ac.uk><CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com><CALthepzPycvfecN9Ln8fvL6Q3PYR0HEbqfAfD9Ysa770E3dsJQ@mail.gmail.com>
	<CA+P6arkm11zAB3du8JVKxcEGh-5XXqFKMpsVa8W6w6qxAVcSLA@mail.gmail.com>
Message-ID: <BLU150-ds52105839586554A9B29258EF80@phx.gbl>

I agree with you 100%.

I have met problems this week in working with the SPICE code too, to the 
extent that I delayed the whole idea till I have more suitable time to 
reimplement it myself.

Amr

--------------------------------------------------
From: "Spencer Bliven" <sbliven at ucsd.edu>
Sent: Wednesday, October 05, 2011 7:39 PM
To: "Andreas Prlic" <andreas at sdsc.edu>
Cc: <biojava-l at lists.open-bio.org>
Subject: Re: [Biojava-l] NullPointerException when 
usingAlignments.getMultipleSequenceAlignment

> In the current SVN code (and therefor probably Biojava 3.0.2),
> CookbookMSA.java includes that import statement but is otherwise identical
> to the wiki version. It runs just fine for me. Probably updating to 
> Biojava
> 3.0.2 will fix the null pointer exception.
>
> This does highlight the problem of keeping the wiki synchronized with the
> current BioJava version. Ideally, part of the release process could 
> include
> automated updating of the wiki cookbook from the SVN code, with older
> versions available as a reference. However, I'm not sure that anyone would
> be willing to set up such a complex release process.
>
> -Spencer
>
> On Wed, Oct 5, 2011 at 10:21, Andreas Prlic <andreas at sdsc.edu> wrote:
>
>> Hi Hannes,
>>
>> > I noticed in an earlier discussion, there was some talk about this too
>> > (3-4 months ago, perhaps) and something about a possible fix in SVN.
>> > when will it be released on the maven server?
>>
>> What version are you on? We released Maven 3.0.2 just recently..
>>
>> Andreas
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 


From biojava at hannes.oib.com  Wed Oct  5 19:22:13 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 5 Oct 2011 21:22:13 +0200
Subject: [Biojava-l] NullPointerException when using
	Alignments.getMultipleSequenceAlignment
In-Reply-To: <CA+P6arkm11zAB3du8JVKxcEGh-5XXqFKMpsVa8W6w6qxAVcSLA@mail.gmail.com>
References: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com>
	<CAB1D7DF.1E3D%hk3@sanger.ac.uk>
	<CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com>
	<CALthepzPycvfecN9Ln8fvL6Q3PYR0HEbqfAfD9Ysa770E3dsJQ@mail.gmail.com>
	<CA+P6arkm11zAB3du8JVKxcEGh-5XXqFKMpsVa8W6w6qxAVcSLA@mail.gmail.com>
Message-ID: <CAPXi2m=gHua1ZThqSFE+_zcP-KoCtT1dZ2hsD3sDZQgG6Bvynw@mail.gmail.com>

2011/10/5 Spencer Bliven <sbliven at ucsd.edu>:
> In the current SVN code (and therefor probably Biojava 3.0.2),
> CookbookMSA.java includes that import statement but is otherwise identical
> to the wiki version. It runs just fine for me. Probably updating to Biojava
> 3.0.2 will fix the null pointer exception.

I installed it via Maven just last week - so I guess it should be on
3.0.2 - I'll check tomorrow.

Anyhow, the problem isn't the wiki (I already updated that, btw) but
the fact that it seems to work with Protein Sequences, but when I use
my DNA sequences, it breaks.
If you go to my first post, I copied my code there (just add a wrapper
main that supplies a valid fasta file as parameter)

Hannes


From andreas at sdsc.edu  Wed Oct  5 19:30:41 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 5 Oct 2011 12:30:41 -0700
Subject: [Biojava-l] NullPointerException when using
	Alignments.getMultipleSequenceAlignment
In-Reply-To: <CAPXi2m=gHua1ZThqSFE+_zcP-KoCtT1dZ2hsD3sDZQgG6Bvynw@mail.gmail.com>
References: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com>
	<CAB1D7DF.1E3D%hk3@sanger.ac.uk>
	<CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com>
	<CALthepzPycvfecN9Ln8fvL6Q3PYR0HEbqfAfD9Ysa770E3dsJQ@mail.gmail.com>
	<CA+P6arkm11zAB3du8JVKxcEGh-5XXqFKMpsVa8W6w6qxAVcSLA@mail.gmail.com>
	<CAPXi2m=gHua1ZThqSFE+_zcP-KoCtT1dZ2hsD3sDZQgG6Bvynw@mail.gmail.com>
Message-ID: <CALthepyBzyVUFG0+gDgrgGAXBoY7jM=F4T_1D7xZbSscaXRd2g@mail.gmail.com>

Can you provide the fasta file? otherwise this is difficult to reproduce...

Andreas

On Wed, Oct 5, 2011 at 12:22 PM, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> 2011/10/5 Spencer Bliven <sbliven at ucsd.edu>:
>> In the current SVN code (and therefor probably Biojava 3.0.2),
>> CookbookMSA.java includes that import statement but is otherwise identical
>> to the wiki version. It runs just fine for me. Probably updating to Biojava
>> 3.0.2 will fix the null pointer exception.
>
> I installed it via Maven just last week - so I guess it should be on
> 3.0.2 - I'll check tomorrow.
>
> Anyhow, the problem isn't the wiki (I already updated that, btw) but
> the fact that it seems to work with Protein Sequences, but when I use
> my DNA sequences, it breaks.
> If you go to my first post, I copied my code there (just add a wrapper
> main that supplies a valid fasta file as parameter)
>
> Hannes
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From biojava at hannes.oib.com  Wed Oct  5 19:34:38 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 5 Oct 2011 21:34:38 +0200
Subject: [Biojava-l] NullPointerException when using
	Alignments.getMultipleSequenceAlignment
In-Reply-To: <CALthepyBzyVUFG0+gDgrgGAXBoY7jM=F4T_1D7xZbSscaXRd2g@mail.gmail.com>
References: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com>
	<CAB1D7DF.1E3D%hk3@sanger.ac.uk>
	<CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com>
	<CALthepzPycvfecN9Ln8fvL6Q3PYR0HEbqfAfD9Ysa770E3dsJQ@mail.gmail.com>
	<CA+P6arkm11zAB3du8JVKxcEGh-5XXqFKMpsVa8W6w6qxAVcSLA@mail.gmail.com>
	<CAPXi2m=gHua1ZThqSFE+_zcP-KoCtT1dZ2hsD3sDZQgG6Bvynw@mail.gmail.com>
	<CALthepyBzyVUFG0+gDgrgGAXBoY7jM=F4T_1D7xZbSscaXRd2g@mail.gmail.com>
Message-ID: <CAPXi2m=BY2uym5hggHh75rU9o36LLV9276uFDQQ96xwdsa098w@mail.gmail.com>

On Wed, Oct 5, 2011 at 21:30, Andreas Prlic <andreas at sdsc.edu> wrote:
> Can you provide the fasta file? otherwise this is difficult to reproduce...
>
> Andreas

Unfortunately, the files in question are under NDA - does it work with
other fasta files? I could not get it to work with the files I tried.

Hannes


From andreas at sdsc.edu  Thu Oct  6 00:29:11 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 5 Oct 2011 17:29:11 -0700
Subject: [Biojava-l] NullPointerException when using
	Alignments.getMultipleSequenceAlignment
In-Reply-To: <CAPXi2m=BY2uym5hggHh75rU9o36LLV9276uFDQQ96xwdsa098w@mail.gmail.com>
References: <CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w@mail.gmail.com>
	<CAB1D7DF.1E3D%hk3@sanger.ac.uk>
	<CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q@mail.gmail.com>
	<CALthepzPycvfecN9Ln8fvL6Q3PYR0HEbqfAfD9Ysa770E3dsJQ@mail.gmail.com>
	<CA+P6arkm11zAB3du8JVKxcEGh-5XXqFKMpsVa8W6w6qxAVcSLA@mail.gmail.com>
	<CAPXi2m=gHua1ZThqSFE+_zcP-KoCtT1dZ2hsD3sDZQgG6Bvynw@mail.gmail.com>
	<CALthepyBzyVUFG0+gDgrgGAXBoY7jM=F4T_1D7xZbSscaXRd2g@mail.gmail.com>
	<CAPXi2m=BY2uym5hggHh75rU9o36LLV9276uFDQQ96xwdsa098w@mail.gmail.com>
Message-ID: <CALthepwAgkbSdyicc=tP1CwzVsXGypN0FPc+kGGvuKgkecq7wA@mail.gmail.com>

> Unfortunately, the files in question are under NDA - does it work with
> other fasta files? I could not get it to work with the files I tried.

I just wrote a junit test for DNA alignments and it works for me. DNA
alignments by default are using the nuc-4_4 substitution matrix for
the alignment. It contains the following  columns.    A   T   G   C
S   W   R   Y   K   M   B   V   H   D   N

Does your FASTA file contain any characters that are not in this list?

Andreas


From biojava at hannes.oib.com  Thu Oct  6 07:32:59 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 6 Oct 2011 09:32:59 +0200
Subject: [Biojava-l] losing meta-info after multiple sequence alignment
Message-ID: <CAPXi2mn-tbGzpShDiYD=ghCo123_a4iM5TPnRsBjnbCNHFd9Bg@mail.gmail.com>

Hi again!

So, my MSA is now working, thanks for the help so far.

What I ran into now is that most of the meta-information of a Sequence
seems to get lost during the MSA step.

e.g.:
I'd like to attach the string from the fasta file (description,
header, whatever it is called) to the sequence and keep it attached
for further use after the MSA step.

1) shouldn't the fasta reader automatically populate this info? which
is the correct field (OriginalHeader or Description or something
else)?
2) the MSA step seems to throw away all meta info. I attached the
string as OriginalHeader before starting the MSA, and afterwards it is
"null"

Thanks,
Hannes


From biojava at hannes.oib.com  Thu Oct  6 08:07:17 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 6 Oct 2011 10:07:17 +0200
Subject: [Biojava-l] losing meta-info after multiple sequence alignment
In-Reply-To: <CAPXi2mn-tbGzpShDiYD=ghCo123_a4iM5TPnRsBjnbCNHFd9Bg@mail.gmail.com>
References: <CAPXi2mn-tbGzpShDiYD=ghCo123_a4iM5TPnRsBjnbCNHFd9Bg@mail.gmail.com>
Message-ID: <CAPXi2mm4WAYrLFMnAcU7iB+oezS=GXqCEbsdwZXTgbW=7_GS3w@mail.gmail.com>

On Thu, Oct 6, 2011 at 09:32, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> Hi again!
> What I ran into now is that most of the meta-information of a Sequence
> seems to get lost during the MSA step.

Okay, that was something caused by following another cookbook script
(that, unfortunately, has absolutely no docs or comments) - I found
the getOriginalSequence() method, can work with that. Thanks!

Hannes



From biojava at hannes.oib.com  Thu Oct  6 10:37:23 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 6 Oct 2011 12:37:23 +0200
Subject: [Biojava-l] losing meta-info after multiple sequence alignment
In-Reply-To: <CAB2FB9A.F0E0%hwillis@scripps.edu>
References: <CAPXi2mm4WAYrLFMnAcU7iB+oezS=GXqCEbsdwZXTgbW=7_GS3w@mail.gmail.com>
	<CAB2FB9A.F0E0%hwillis@scripps.edu>
Message-ID: <CAPXi2mk=Zomg3HmxBET3b95ujJW8-UBfawJ0byPVWUXrMf5Sbg@mail.gmail.com>

Thanks, I'll try to add what I find out. It's a wiki after all. I'll
just ask the mailing list if things are unclear before I add stuff to
the wiki.

One thing that bugged me just now, and since I can't find documentation on it:

Why is a sequence indexed by 1-(n+1) instead of 0-n? That's rather
un-java-like, especially since you just get an OutOfBoundsException,
and the range is not specified in the javadoc, or I could not find it
easily in the complex class hierarchy.

Hannes

2011/10/6 Scooter Willis <HWillis at scripps.edu>:
> Hannes
>
> As you can tell we need to improve the cookbook examples. Since you are
> going through that process would welcome any contributions you can make.
>
> Thanks
>
> Scooter
>
> On 10/6/11 4:07 AM, "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com>
> wrote:
>
>>On Thu, Oct 6, 2011 at 09:32, Hannes Brandst?tter-M?ller
>><biojava at hannes.oib.com> wrote:
>>> Hi again!
>>> What I ran into now is that most of the meta-information of a Sequence
>>> seems to get lost during the MSA step.
>>
>>Okay, that was something caused by following another cookbook script
>>(that, unfortunately, has absolutely no docs or comments) - I found
>>the getOriginalSequence() method, can work with that. Thanks!
>>
>>Hannes
>>
>>_______________________________________________
>>Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>



From HWillis at scripps.edu  Thu Oct  6 10:32:10 2011
From: HWillis at scripps.edu (Scooter Willis)
Date: Thu, 6 Oct 2011 06:32:10 -0400
Subject: [Biojava-l] losing meta-info after multiple sequence alignment
In-Reply-To: <CAPXi2mm4WAYrLFMnAcU7iB+oezS=GXqCEbsdwZXTgbW=7_GS3w@mail.gmail.com>
Message-ID: <CAB2FB9A.F0E0%hwillis@scripps.edu>

Hannes

As you can tell we need to improve the cookbook examples. Since you are
going through that process would welcome any contributions you can make.

Thanks

Scooter

On 10/6/11 4:07 AM, "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com>
wrote:

>On Thu, Oct 6, 2011 at 09:32, Hannes Brandst?tter-M?ller
><biojava at hannes.oib.com> wrote:
>> Hi again!
>> What I ran into now is that most of the meta-information of a Sequence
>> seems to get lost during the MSA step.
>
>Okay, that was something caused by following another cookbook script
>(that, unfortunately, has absolutely no docs or comments) - I found
>the getOriginalSequence() method, can work with that. Thanks!
>
>Hannes
>
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/biojava-l




From andreas.prlic at gmail.com  Thu Oct  6 15:35:22 2011
From: andreas.prlic at gmail.com (Andreas Prlic)
Date: Thu, 6 Oct 2011 08:35:22 -0700
Subject: [Biojava-l] BioJava Help
In-Reply-To: <CA+ggGe4Efh5c8-FFFE3hS12E-4ergVcBBn2FQvT1juZTSUmpng@mail.gmail.com>
References: <CA+ggGe4Efh5c8-FFFE3hS12E-4ergVcBBn2FQvT1juZTSUmpng@mail.gmail.com>
Message-ID: <CALthepw8W_T0B9dSAqQOnFU1UnZjLUhqS-8dVoKd60xB9SpmCA@mail.gmail.com>

Hi Omer,

We are having problems with the anonymous SVN server quite often. I
recommend trying the git copy at github, or their SVN interface, or
using Maven to install it.

http://www.biojava.org/wiki/CVS_to_SVN_Migration

Andreas

On Thu, Oct 6, 2011 at 1:56 AM, Omer Eilam <omereila at post.tau.ac.il> wrote:
> Dear Andreas,
>
> I wish to install BioJava for my eclipse IDE.
> I followed all the instructions in the website
> http://www.biojava.org/wiki/BioJava3_eclipse.
> I currently have problems with the last step. I create a new Maven
> project, but when I try to type /biojava/biojava-live/trunk in the SCM
> URL, I get an "invalid URL" error.
> Please let me know what seems to be the problem and how can I fix it.
>
> Thanks much!
> omer
>
> --
> Omer Eilam
> Complex Network Systems
> Prof. Eytan Ruppin
> Tel-Aviv University
> http://cns.cs.tau.ac.il/
>


From sbliven at ucsd.edu  Thu Oct  6 18:29:06 2011
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Thu, 6 Oct 2011 11:29:06 -0700
Subject: [Biojava-l] losing meta-info after multiple sequence alignment
In-Reply-To: <CAPXi2mk=Zomg3HmxBET3b95ujJW8-UBfawJ0byPVWUXrMf5Sbg@mail.gmail.com>
References: <CAPXi2mm4WAYrLFMnAcU7iB+oezS=GXqCEbsdwZXTgbW=7_GS3w@mail.gmail.com>
	<CAB2FB9A.F0E0%hwillis@scripps.edu>
	<CAPXi2mk=Zomg3HmxBET3b95ujJW8-UBfawJ0byPVWUXrMf5Sbg@mail.gmail.com>
Message-ID: <CA+P6arkEx4RTGWo=HadaCX1v41FBv-CiPUudq7LLo+ooOCXR9Q@mail.gmail.com>

I think that 1-based indexing was chosen because that's what's used in
genome databases like GenBank. Thus gene offsets from outside data sources
can be used directly without subtracting 1. That said, almost every time I
write code using sequences I get off-by-one errors, so I understand your
frustration. We should definitely improve documentation so that every method
that takes 1-based indexes are clearly marked.

-Spencer

On Thu, Oct 6, 2011 at 03:37, Hannes Brandst?tter-M?ller <
biojava at hannes.oib.com> wrote:

> Thanks, I'll try to add what I find out. It's a wiki after all. I'll
> just ask the mailing list if things are unclear before I add stuff to
> the wiki.
>
> One thing that bugged me just now, and since I can't find documentation on
> it:
>
> Why is a sequence indexed by 1-(n+1) instead of 0-n? That's rather
> un-java-like, especially since you just get an OutOfBoundsException,
> and the range is not specified in the javadoc, or I could not find it
> easily in the complex class hierarchy.
>
> Hannes
>
> 2011/10/6 Scooter Willis <HWillis at scripps.edu>:
> > Hannes
> >
> > As you can tell we need to improve the cookbook examples. Since you are
> > going through that process would welcome any contributions you can make.
> >
> > Thanks
> >
> > Scooter
> >
> > On 10/6/11 4:07 AM, "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com
> >
> > wrote:
> >
> >>On Thu, Oct 6, 2011 at 09:32, Hannes Brandst?tter-M?ller
> >><biojava at hannes.oib.com> wrote:
> >>> Hi again!
> >>> What I ran into now is that most of the meta-information of a Sequence
> >>> seems to get lost during the MSA step.
> >>
> >>Okay, that was something caused by following another cookbook script
> >>(that, unfortunately, has absolutely no docs or comments) - I found
> >>the getOriginalSequence() method, can work with that. Thanks!
> >>
> >>Hannes
> >>
> >>_______________________________________________
> >>Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> >
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From andreas.prlic at gmail.com  Mon Oct 10 01:58:43 2011
From: andreas.prlic at gmail.com (Andreas Prlic)
Date: Sun, 9 Oct 2011 18:58:43 -0700
Subject: [Biojava-l] BioJava Help
In-Reply-To: <CA+ggGe7U1VevV+R7gyW1gFxns-zjke86F=h450z0XsRywzLtMw@mail.gmail.com>
References: <CA+ggGe4Efh5c8-FFFE3hS12E-4ergVcBBn2FQvT1juZTSUmpng@mail.gmail.com>
	<CALthepw8W_T0B9dSAqQOnFU1UnZjLUhqS-8dVoKd60xB9SpmCA@mail.gmail.com>
	<CA+ggGe7U1VevV+R7gyW1gFxns-zjke86F=h450z0XsRywzLtMw@mail.gmail.com>
Message-ID: <CALthepyXMb9uy72cw-ORaBGnUf6LvuEHrurY+y2_4GaduvjE_A@mail.gmail.com>

Hi Omer,

Our recommendation nowadays for working with Blast is to get XML
output and simply parse that. Depending on what you need that will
give you more details than the parser that is in the BioJava 1.8
(legacy) project. (if you still want to give that one a try, there is
a cookbook page for it)

Andreas


On Sun, Oct 9, 2011 at 2:26 AM, Omer Eilam <omereila at post.tau.ac.il> wrote:
> I eventually succeeded in importing Biojava.
> I read in the paper that there is a parser for BLAST - where can I get
> more information/API on this?
>
> Thanks!
> omer
>
> On Thu, Oct 6, 2011 at 5:35 PM, Andreas Prlic <andreas.prlic at gmail.com> wrote:
>> Hi Omer,
>>
>> We are having problems with the anonymous SVN server quite often. I
>> recommend trying the git copy at github, or their SVN interface, or
>> using Maven to install it.
>>
>> http://www.biojava.org/wiki/CVS_to_SVN_Migration
>>
>> Andreas
>>
>> On Thu, Oct 6, 2011 at 1:56 AM, Omer Eilam <omereila at post.tau.ac.il> wrote:
>>> Dear Andreas,
>>>
>>> I wish to install BioJava for my eclipse IDE.
>>> I followed all the instructions in the website
>>> http://www.biojava.org/wiki/BioJava3_eclipse.
>>> I currently have problems with the last step. I create a new Maven
>>> project, but when I try to type /biojava/biojava-live/trunk in the SCM
>>> URL, I get an "invalid URL" error.
>>> Please let me know what seems to be the problem and how can I fix it.
>>>
>>> Thanks much!
>>> omer
>>>
>>> --
>>> Omer Eilam
>>> Complex Network Systems
>>> Prof. Eytan Ruppin
>>> Tel-Aviv University
>>> http://cns.cs.tau.ac.il/
>>>
>>
>
>
>
> --
> Omer Eilam
> Complex Network Systems
> Prof. Eytan Ruppin
> Tel-Aviv University
> http://cns.cs.tau.ac.il/
>


From shakunb at uom.ac.mu  Mon Oct 10 09:03:34 2011
From: shakunb at uom.ac.mu (Shakuntala Baichoo)
Date: Mon, 10 Oct 2011 13:03:34 +0400
Subject: [Biojava-l] Biojava-l Digest, Vol 105, Issue 5
In-Reply-To: <mailman.7.1318003203.13809.biojava-l@lists.open-bio.org>
References: <mailman.7.1318003203.13809.biojava-l@lists.open-bio.org>
Message-ID: <CAKpuL5gkmSQk3hJSnDdSRqovmnu3x_BaNPG1evLT7p5ugRLA7Q@mail.gmail.com>

Does anyone know how to find codon usage from data in a genbank file or embl
file.

Thanks
Shakun

On Fri, Oct 7, 2011 at 8:00 PM, <biojava-l-request at lists.open-bio.org>wrote:

> Send Biojava-l mailing list submissions to
>        biojava-l at lists.open-bio.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://lists.open-bio.org/mailman/listinfo/biojava-l
> or, via email, send a message with subject or body 'help' to
>        biojava-l-request at lists.open-bio.org
>
> You can reach the person managing the list at
>        biojava-l-owner at lists.open-bio.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Biojava-l digest..."
>
>
> Today's Topics:
>
>   1. Re: losing meta-info after multiple sequence alignment
>      (Spencer Bliven)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 6 Oct 2011 11:29:06 -0700
> From: Spencer Bliven <sbliven at ucsd.edu>
> Subject: Re: [Biojava-l] losing meta-info after multiple sequence
>        alignment
> To: Hannes Brandst?tter-M?ller <biojava at hannes.oib.com>
> Cc: "Biojava-l at lists.open-bio.org" <biojava-l at lists.open-bio.org>,
>        Scooter Willis <HWillis at scripps.edu>
> Message-ID:
>        <CA+P6arkEx4RTGWo=HadaCX1v41FBv-CiPUudq7LLo+ooOCXR9Q at mail.gmail.com
> >
> Content-Type: text/plain; charset=UTF-8
>
> I think that 1-based indexing was chosen because that's what's used in
> genome databases like GenBank. Thus gene offsets from outside data sources
> can be used directly without subtracting 1. That said, almost every time I
> write code using sequences I get off-by-one errors, so I understand your
> frustration. We should definitely improve documentation so that every
> method
> that takes 1-based indexes are clearly marked.
>
> -Spencer
>
> On Thu, Oct 6, 2011 at 03:37, Hannes Brandst?tter-M?ller <
> biojava at hannes.oib.com> wrote:
>
> > Thanks, I'll try to add what I find out. It's a wiki after all. I'll
> > just ask the mailing list if things are unclear before I add stuff to
> > the wiki.
> >
> > One thing that bugged me just now, and since I can't find documentation
> on
> > it:
> >
> > Why is a sequence indexed by 1-(n+1) instead of 0-n? That's rather
> > un-java-like, especially since you just get an OutOfBoundsException,
> > and the range is not specified in the javadoc, or I could not find it
> > easily in the complex class hierarchy.
> >
> > Hannes
> >
> > 2011/10/6 Scooter Willis <HWillis at scripps.edu>:
> > > Hannes
> > >
> > > As you can tell we need to improve the cookbook examples. Since you are
> > > going through that process would welcome any contributions you can
> make.
> > >
> > > Thanks
> > >
> > > Scooter
> > >
> > > On 10/6/11 4:07 AM, "Hannes Brandst?tter-M?ller" <
> biojava at hannes.oib.com
> > >
> > > wrote:
> > >
> > >>On Thu, Oct 6, 2011 at 09:32, Hannes Brandst?tter-M?ller
> > >><biojava at hannes.oib.com> wrote:
> > >>> Hi again!
> > >>> What I ran into now is that most of the meta-information of a
> Sequence
> > >>> seems to get lost during the MSA step.
> > >>
> > >>Okay, that was something caused by following another cookbook script
> > >>(that, unfortunately, has absolutely no docs or comments) - I found
> > >>the getOriginalSequence() method, can work with that. Thanks!
> > >>
> > >>Hannes
> > >>
> > >>_______________________________________________
> > >>Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > >>http://lists.open-bio.org/mailman/listinfo/biojava-l
> > >
> > >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
>
>
> ------------------------------
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
> End of Biojava-l Digest, Vol 105, Issue 5
> *****************************************
>

Email Disclaimer:
This email and all its contents are subject to the disclaimer at http://www.uom.ac.mu/emaildisclaimer  



From tariq_cp at hotmail.com  Mon Oct 10 16:27:27 2011
From: tariq_cp at hotmail.com (Muhammad Tariq Pervez)
Date: Mon, 10 Oct 2011 16:27:27 +0000
Subject: [Biojava-l] Biojava-l Digest, Vol 105, Issue 2
In-Reply-To: <mailman.3.1317830404.30987.biojava-l@lists.open-bio.org>
References: <mailman.3.1317830404.30987.biojava-l@lists.open-bio.org>
Message-ID: <SNT131-W377F9853A3A2D61396BF30FCFD0@phx.gbl>


Yes, the issue was also faced by me. 
I also highlighted the solution.

The solution has also been uploaded/updated in SVN.


Muhammad Tariq Pervez

PhD Scholar


> From: biojava-l-request at lists.open-bio.org
> Subject: Biojava-l Digest, Vol 105, Issue 2
> To: biojava-l at lists.open-bio.org
> Date: Wed, 5 Oct 2011 12:00:04 -0400
> 
> Send Biojava-l mailing list submissions to
> 	biojava-l at lists.open-bio.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://lists.open-bio.org/mailman/listinfo/biojava-l
> or, via email, send a message with subject or body 'help' to
> 	biojava-l-request at lists.open-bio.org
> 
> You can reach the person managing the list at
> 	biojava-l-owner at lists.open-bio.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Biojava-l digest..."
> 
> 
> Today's Topics:
> 
>    1. NullPointerException when using
>       Alignments.getMultipleSequenceAlignment (Hannes Brandst?tter-M?ller)
>    2. Re: NullPointerException when using
>       Alignments.getMultipleSequenceAlignment (Hannes Brandst?tter-M?ller)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 5 Oct 2011 09:41:57 +0200
> From: Hannes Brandst?tter-M?ller 	<biojava at hannes.oib.com>
> Subject: [Biojava-l] NullPointerException when using
> 	Alignments.getMultipleSequenceAlignment
> To: biojava-l at lists.open-bio.org
> Message-ID:
> 	<CAPXi2mnpLujT=dvEQkLxFpih1sv6pe_-vob2vJJd-axOu4jr_w at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hello!
> 
> I tried to follow http://biojava.org/wiki/BioJava:CookBook3:MSA, but
> when I run it, I get:
> 
> java.util.concurrent.ExecutionException: java.lang.NullPointerException
> 	at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
> 	at java.util.concurrent.FutureTask.get(FutureTask.java:83)
> 	at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
> 	at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
> 	at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173)
> 
>  What could I be doing wrong?
> 
> (
> on the cookbook page, there is also an import missing:
> import org.biojava3.alignment.Alignments;
> )
> -> then the cookbook runs, but my code does not
> 
> private static void processFile(String filename) {
>         try {
>             FileInputStream inStream = new FileInputStream(filename);
>             FastaReader<DNASequence, NucleotideCompound> fastaReader =
>                     new FastaReader<DNASequence, NucleotideCompound>(
>                     inStream,
>                     new GenericFastaHeaderParser<DNASequence,
> NucleotideCompound>(),
>                     new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
>             LinkedHashMap<String, DNASequence> b = fastaReader.process();
> 
>             List<DNASequence> sequences = new ArrayList<DNASequence>();
>             for (Entry<String, DNASequence> entry : b.entrySet()) {
>                 if (sequences.size() < 5) {
>                     sequences.add(entry.getValue());
>                 }
>                 System.out.println(entry.getValue());
>             }
> 
>             Profile<DNASequence, NucleotideCompound> profile =
> Alignments.getMultipleSequenceAlignment(sequences);
>             System.out.printf("Clustalw:%n%s%n", profile);
> 
>             ConcurrencyTools.shutdown();
>         } catch (Exception ex) {
>             Logger.getLogger(App.class.getName()).log(Level.SEVERE, null, ex);
>         }
>     }
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Wed, 5 Oct 2011 10:50:33 +0200
> From: Hannes Brandst?tter-M?ller 	<biojava at hannes.oib.com>
> Subject: Re: [Biojava-l] NullPointerException when using
> 	Alignments.getMultipleSequenceAlignment
> To: biojava-l at lists.open-bio.org
> Message-ID:
> 	<CAPXi2mnRE07CAtbUV6bTB8G7wHzSkK543GrB8dc7s4JoUzkp=Q at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi!
> 
> I read the sequence from a fasta file.
> 
> FileInputStream inStream = new FileInputStream(filename);
>             FastaReader<DNASequence, NucleotideCompound> fastaReader =
>                     new FastaReader<DNASequence, NucleotideCompound>(
>                     inStream,
>                     new GenericFastaHeaderParser<DNASequence,
> NucleotideCompound>(),
>                     new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
>             LinkedHashMap<String, DNASequence> b = fastaReader.process();
> 
> and then use
> List<DNASequence> sequences = new ArrayList<DNASequence>();
>             for (Entry<String, DNASequence> entry : b.entrySet()) {
>                 sequences.add(entry.getValue());
> }
> 
> to get the required list of DNA sequences.
> 
> I noticed in an earlier discussion, there was some talk about this too
> (3-4 months ago, perhaps) and something about a possible fix in SVN.
> when will it be released on the maven server?
> 
> Hannes
> 
> On Wed, Oct 5, 2011 at 10:46, Hashem Koohy <hk3 at sanger.ac.uk> wrote:
> > Hi Hannes,
> > It seems to me it doesn't like your ?dna Sequence!
> > Is your sequence in the following format?
> >
> > Sequence dnaSeq = DNATools.createDNASequence("acccgggttttacagt", "id");
> >
> > Good luck
> > Hashem
> >
> > On 05/10/2011 08:41, "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com>
> > wrote:
> >
> >> Hello!
> >>
> >> I tried to follow http://biojava.org/wiki/BioJava:CookBook3:MSA, but
> >> when I run it, I get:
> >>
> >> java.util.concurrent.ExecutionException: java.lang.NullPointerException
> >> at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
> >> at java.util.concurrent.FutureTask.get(FutureTask.java:83)
> >> at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
> >> at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
> >> at
> >> org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java
> >> :173)
> >>
> >> ?What could I be doing wrong?
> >>
> >> (
> >> on the cookbook page, there is also an import missing:
> >> import org.biojava3.alignment.Alignments;
> >> )
> >> -> then the cookbook runs, but my code does not
> >>
> >> private static void processFile(String filename) {
> >> ? ? ? ? try {
> >> ? ? ? ? ? ? FileInputStream inStream = new FileInputStream(filename);
> >> ? ? ? ? ? ? FastaReader<DNASequence, NucleotideCompound> fastaReader =
> >> ? ? ? ? ? ? ? ? ? ? new FastaReader<DNASequence, NucleotideCompound>(
> >> ? ? ? ? ? ? ? ? ? ? inStream,
> >> ? ? ? ? ? ? ? ? ? ? new GenericFastaHeaderParser<DNASequence,
> >> NucleotideCompound>(),
> >> ? ? ? ? ? ? ? ? ? ? new
> >> DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
> >> ? ? ? ? ? ? LinkedHashMap<String, DNASequence> b = fastaReader.process();
> >>
> >> ? ? ? ? ? ? List<DNASequence> sequences = new ArrayList<DNASequence>();
> >> ? ? ? ? ? ? for (Entry<String, DNASequence> entry : b.entrySet()) {
> >> ? ? ? ? ? ? ? ? if (sequences.size() < 5) {
> >> ? ? ? ? ? ? ? ? ? ? sequences.add(entry.getValue());
> >> ? ? ? ? ? ? ? ? }
> >> ? ? ? ? ? ? ? ? System.out.println(entry.getValue());
> >> ? ? ? ? ? ? }
> >>
> >> ? ? ? ? ? ? Profile<DNASequence, NucleotideCompound> profile =
> >> Alignments.getMultipleSequenceAlignment(sequences);
> >> ? ? ? ? ? ? System.out.printf("Clustalw:%n%s%n", profile);
> >>
> >> ? ? ? ? ? ? ConcurrencyTools.shutdown();
> >> ? ? ? ? } catch (Exception ex) {
> >> ? ? ? ? ? ? Logger.getLogger(App.class.getName()).log(Level.SEVERE, null, ex);
> >> ? ? ? ? }
> >> ? ? }
> >> _______________________________________________
> >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> > -------------------------------
> > Hashem Koohy
> > PhD
> > Postdoctoral Fellow,
> > Sanger Institute,
> > Cambridge
> > Mobile: 07515425433
> >
> >
> >
> >
> > --
> > ?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.
> >
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 
> End of Biojava-l Digest, Vol 105, Issue 2
> *****************************************
 		 	   		  


From xue.vin at gmail.com  Tue Oct 11 00:39:52 2011
From: xue.vin at gmail.com (Vincent Xue)
Date: Mon, 10 Oct 2011 20:39:52 -0400
Subject: [Biojava-l] Stockholm Parser Implementation?
Message-ID: <CAN9vMjktBR0ySLj0hFtGZhycO+AETLggsmJYs335bKEcjka4dQ@mail.gmail.com>

Hi,

I was wondering if there has been any work on developing a Stockholm
1.0 parser?

Thanks!


From andreas.prlic at gmail.com  Tue Oct 11 22:51:48 2011
From: andreas.prlic at gmail.com (Andreas Prlic)
Date: Tue, 11 Oct 2011 15:51:48 -0700
Subject: [Biojava-l] BioJava Help
In-Reply-To: <CA+ggGe69q1QvRHQs2xe923XrWcnKBBu9XUB91aGo4cDoLv39wA@mail.gmail.com>
References: <CA+ggGe4Efh5c8-FFFE3hS12E-4ergVcBBn2FQvT1juZTSUmpng@mail.gmail.com>
	<CALthepw8W_T0B9dSAqQOnFU1UnZjLUhqS-8dVoKd60xB9SpmCA@mail.gmail.com>
	<CA+ggGe7U1VevV+R7gyW1gFxns-zjke86F=h450z0XsRywzLtMw@mail.gmail.com>
	<CALthepyXMb9uy72cw-ORaBGnUf6LvuEHrurY+y2_4GaduvjE_A@mail.gmail.com>
	<CA+ggGe69q1QvRHQs2xe923XrWcnKBBu9XUB91aGo4cDoLv39wA@mail.gmail.com>
Message-ID: <CALthepyTq2s7U6Fm2hrStvRr=vo0LvNtu6SfZU5ERPTc4ayfVw@mail.gmail.com>

Hi Omer,

please keep such questions on the public list. Chances are high that
if you are struggling with something, somebody else is having the same
problem as well.

I wasactually talking about BioJava 1.8, the previous version of
BioJava. It is still available and the cookbook page that I meant is
here:
http://biojava.org/wiki/BioJava:CookBook:Blast:Parser

About Maven: It is probably best to start with a new project in your
favorite IDE and set it up as a Maven project that depends on BioJava.
(i.e. add the BioJava repository to the pom configuraiton). If you
think this is difficult, we can/should set up a documentation page
that explains those first steps.

Andreas



On Tue, Oct 11, 2011 at 6:34 AM, Omer Eilam <omereila at post.tau.ac.il> wrote:
> Are you referring to the BlastXMLQuery class? because I see in the API
> that it contains only one method.
> Also, I am not familiar with using Maven, I see the various biojava
> packages in the eclipse project explorer, but I don't know how to
> create a new class (i.e. do I need imports and stuff?)
>
> Thanks again!
> omer
>
> On Mon, Oct 10, 2011 at 3:58 AM, Andreas Prlic <andreas.prlic at gmail.com> wrote:
>> Hi Omer,
>>
>> Our recommendation nowadays for working with Blast is to get XML
>> output and simply parse that. Depending on what you need that will
>> give you more details than the parser that is in the BioJava 1.8
>> (legacy) project. (if you still want to give that one a try, there is
>> a cookbook page for it)
>>
>> Andreas
>>
>>
>> On Sun, Oct 9, 2011 at 2:26 AM, Omer Eilam <omereila at post.tau.ac.il> wrote:
>>> I eventually succeeded in importing Biojava.
>>> I read in the paper that there is a parser for BLAST - where can I get
>>> more information/API on this?
>>>
>>> Thanks!
>>> omer
>>>
>>> On Thu, Oct 6, 2011 at 5:35 PM, Andreas Prlic <andreas.prlic at gmail.com> wrote:
>>>> Hi Omer,
>>>>
>>>> We are having problems with the anonymous SVN server quite often. I
>>>> recommend trying the git copy at github, or their SVN interface, or
>>>> using Maven to install it.
>>>>
>>>> http://www.biojava.org/wiki/CVS_to_SVN_Migration
>>>>
>>>> Andreas
>>>>
>>>> On Thu, Oct 6, 2011 at 1:56 AM, Omer Eilam <omereila at post.tau.ac.il> wrote:
>>>>> Dear Andreas,
>>>>>
>>>>> I wish to install BioJava for my eclipse IDE.
>>>>> I followed all the instructions in the website
>>>>> http://www.biojava.org/wiki/BioJava3_eclipse.
>>>>> I currently have problems with the last step. I create a new Maven
>>>>> project, but when I try to type /biojava/biojava-live/trunk in the SCM
>>>>> URL, I get an "invalid URL" error.
>>>>> Please let me know what seems to be the problem and how can I fix it.
>>>>>
>>>>> Thanks much!
>>>>> omer
>>>>>
>>>>> --
>>>>> Omer Eilam
>>>>> Complex Network Systems
>>>>> Prof. Eytan Ruppin
>>>>> Tel-Aviv University
>>>>> http://cns.cs.tau.ac.il/
>>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> Omer Eilam
>>> Complex Network Systems
>>> Prof. Eytan Ruppin
>>> Tel-Aviv University
>>> http://cns.cs.tau.ac.il/
>>>
>>
>
>
>
> --
> Omer Eilam
> Complex Network Systems
> Prof. Eytan Ruppin
> Tel-Aviv University
> http://cns.cs.tau.ac.il/
>


From andreas.prlic at gmail.com  Wed Oct 12 16:00:14 2011
From: andreas.prlic at gmail.com (Andreas Prlic)
Date: Wed, 12 Oct 2011 09:00:14 -0700
Subject: [Biojava-l] User defined substitution matrix.
In-Reply-To: <CAEqMO2HNFfV+qtWJmp9mxP8JV_WCKu5hfCYkvi_Y3Lpf+XLafw@mail.gmail.com>
References: <CAEqMO2HNFfV+qtWJmp9mxP8JV_WCKu5hfCYkvi_Y3Lpf+XLafw@mail.gmail.com>
Message-ID: <CALthepyPiC6H=929SU2vo3BLxtF0MszzpJMjEgSP1Fyc5NPb_w@mail.gmail.com>

Hi Canan,

Please subscribe to the biojava-l mailing list for sending messages to
the list. Details for how to do that can be found here:

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

About your question:

getResourceAsStream is just opening a stream to a file that is bundled
together with a jar file. There should be no need for you to call that
to get a matrix.

If you want to use any of the (many) standard substitution matrices
that are supported by BioJava you just need to call
SubstitutionMatrixHelper .getMatrixFromAAINDEX(nameOfMatrix)

If you want to work with a matrix that is not yet the AAINDEX
collection of matrices, it depends on how the matrix is represented in
the file. If it is in the same style as in AAINDEX, you can use the
DefaultAAIndexProvider to parse your custom matrix.

Andreas




On Tue, Oct 11, 2011 at 11:09 PM, Canan Has <cananhas at iyte.edu.tr> wrote:
> Dear Dr. Prlic,
> Sorry to bother you, but my mails to biojava forum-nabble are not being
> answered. Even I have been already subscribed, I am getting alerts saying
> your message is in pending list, because you are not subscribed.?Therefore,
> I decided to ?ask my question to you directly. I hope you will answer to me.
> Because, it is so important and urgent.
> Simply,I want to create my own substitution matrix object. I examined the
> source code of SubstitutionMatrixHelper and the related others. I did some
> modifications and took null pointer exception for getResourceAsStream().
> I tried to find out where the directory for getResourceAsStream() has been
> set. At first, I thought the file directory is the resources folder in
> alignment folder. Then, I deleted one of the matrices - pam250 and tried to
> initialize it by calling getPam250() and matrix was created. This leads me
> to think that the developer introduced ftp.ncbi url to ?getResourceAsStream
> to take matrices by name.
> Can you show a way to create my own? Or you can tell me and I can change
> where the url is given and recompile the code.
> Thanks in advance
> Canan Has
> Research Assistant & MSc Student
> Computational Biology & Bioinformatics Lab
> Molecular Biology and Genetics Department
> Izmir Institute of Technology
>



From andreas at sdsc.edu  Wed Oct 12 16:05:58 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 12 Oct 2011 09:05:58 -0700
Subject: [Biojava-l] Stockholm Parser Implementation?
In-Reply-To: <CAN9vMjktBR0ySLj0hFtGZhycO+AETLggsmJYs335bKEcjka4dQ@mail.gmail.com>
References: <CAN9vMjktBR0ySLj0hFtGZhycO+AETLggsmJYs335bKEcjka4dQ@mail.gmail.com>
Message-ID: <CALthepw9K4VWQJRT1pxy+AG1UpQG345i_vQaeavkXce90GR5vw@mail.gmail.com>

Hi Vincent,

I am not aware of parser for that as part of Biojava. It would be
great to have, though. If you want to make a contribution, you would
be more than welcome ...

Andreas



On Mon, Oct 10, 2011 at 5:39 PM, Vincent Xue <xue.vin at gmail.com> wrote:
> Hi,
>
> I was wondering if there has been any work on developing a Stockholm
> 1.0 parser?
>
> Thanks!
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From jprocter at compbio.dundee.ac.uk  Fri Oct 14 09:07:01 2011
From: jprocter at compbio.dundee.ac.uk (Jim Procter)
Date: Fri, 14 Oct 2011 10:07:01 +0100
Subject: [Biojava-l] Stockholm Parser Implementation?
In-Reply-To: <CALthepw9K4VWQJRT1pxy+AG1UpQG345i_vQaeavkXce90GR5vw@mail.gmail.com>
References: <CAN9vMjktBR0ySLj0hFtGZhycO+AETLggsmJYs335bKEcjka4dQ@mail.gmail.com>
	<CALthepw9K4VWQJRT1pxy+AG1UpQG345i_vQaeavkXce90GR5vw@mail.gmail.com>
Message-ID: <4E97FBB5.5090402@compbio.dundee.ac.uk>

On 12/10/2011 17:05, Andreas Prlic wrote:
> Hi Vincent,
>
> I am not aware of parser for that as part of Biojava. It would be
> great to have, though. If you want to make a contribution, you would
> be more than welcome ...
I thought Jules worked on this - he took a look at Jalview's one and 
promptly wrote a better one, IIRC. However, whether it got in to bj3 is 
another matter!  Perhaps asking him nicely would work :)

Jim.




From kern3020 at gmail.com  Tue Oct 18 00:49:17 2011
From: kern3020 at gmail.com (John Kern)
Date: Mon, 17 Oct 2011 17:49:17 -0700
Subject: [Biojava-l] is the tutorial in sync with the latest version?
Message-ID: <CAJ-7iFV0Ac4h-zkLn_Mh5TBX+gWqFPk8+E-s6=G9UF4V4K7w5w@mail.gmail.com>

Hello,

I am not to Biojava and bioinformatics in general. I noticed your latest
release is 3.0.2 but the tutorial reference to the 1.8 release (
http://biojava.org/wiki/BioJava:Tutorial). Does this imply the tutorial is
out of sync with the tutorial?

Regards,
John


From andreas at sdsc.edu  Tue Oct 18 03:11:16 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 17 Oct 2011 20:11:16 -0700
Subject: [Biojava-l] is the tutorial in sync with the latest version?
In-Reply-To: <CAJ-7iFV0Ac4h-zkLn_Mh5TBX+gWqFPk8+E-s6=G9UF4V4K7w5w@mail.gmail.com>
References: <CAJ-7iFV0Ac4h-zkLn_Mh5TBX+gWqFPk8+E-s6=G9UF4V4K7w5w@mail.gmail.com>
Message-ID: <CALthepwyo0ZV5DpKdwTqGYL7T3789u1Zn=UovrZCDTPLMKKBMA@mail.gmail.com>

Hi John,

This Tutorial was written for what is currently the legacy 1.8
release. It would be great if somebody would volunteer and provide
such a tutorial for the current  3.X code base ...

Andreas



On Mon, Oct 17, 2011 at 5:49 PM, John Kern <kern3020 at gmail.com> wrote:
> Hello,
>
> I am not to Biojava and bioinformatics in general. I noticed your latest
> release is 3.0.2 but the tutorial reference to the 1.8 release (
> http://biojava.org/wiki/BioJava:Tutorial). Does this imply the tutorial is
> out of sync with the tutorial?
>
> Regards,
> John
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> 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
-----------------------------------------------------------------------



From biojava at hannes.oib.com  Tue Oct 18 09:46:44 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Tue, 18 Oct 2011 11:46:44 +0200
Subject: [Biojava-l] Multiple Sequence Alignment - Limits?
In-Reply-To: <CAPXi2mkLfYxixwx-Wgein7O62ojXm0w-gEdxYfOBBd1KSO-hPA@mail.gmail.com>
References: <CAPXi2mkLfYxixwx-Wgein7O62ojXm0w-gEdxYfOBBd1KSO-hPA@mail.gmail.com>
Message-ID: <CAPXi2mmErxQ7tbu8kGuszJAq7SQCqywiAyypT+mnRH7L1jZ3xA@mail.gmail.com>

On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> Hi again!
>
> I am quite happy with the Multiple Sequence Alignment, but I noticed
> that there seems to be a limit of 132 Sequences that are present in
> the final alignment - is this some kind of hardcoded limit, or can I
> work around that somehow?
>
> Hannes
>

Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
fasta format. Is there a way to work around that limit?

Hannes



From kern3020 at gmail.com  Tue Oct 18 14:42:54 2011
From: kern3020 at gmail.com (John Kern)
Date: Tue, 18 Oct 2011 07:42:54 -0700
Subject: [Biojava-l] is the tutorial in sync with the latest version?
In-Reply-To: <CALthepwyo0ZV5DpKdwTqGYL7T3789u1Zn=UovrZCDTPLMKKBMA@mail.gmail.com>
References: <CAJ-7iFV0Ac4h-zkLn_Mh5TBX+gWqFPk8+E-s6=G9UF4V4K7w5w@mail.gmail.com>
	<CALthepwyo0ZV5DpKdwTqGYL7T3789u1Zn=UovrZCDTPLMKKBMA@mail.gmail.com>
Message-ID: <CAJ-7iFVbvhsQOqSYMoCcscgN0eWpFNdupxqDQac_z8PBjvBrHw@mail.gmail.com>

Hello Andreas,

On Mon, Oct 17, 2011 at 8:11 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> It would be great if somebody would volunteer and provide
> such a tutorial for the current ?3.X code base ...

Great. Sign me up. I guess the way to proceed is to learn 3.x via the
cookbook and examples. Then return to the tutorial.

-jk



From andreas at sdsc.edu  Tue Oct 18 21:01:05 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 18 Oct 2011 14:01:05 -0700
Subject: [Biojava-l] Multiple Sequence Alignment - Limits?
In-Reply-To: <CAPXi2mmErxQ7tbu8kGuszJAq7SQCqywiAyypT+mnRH7L1jZ3xA@mail.gmail.com>
References: <CAPXi2mkLfYxixwx-Wgein7O62ojXm0w-gEdxYfOBBd1KSO-hPA@mail.gmail.com>
	<CAPXi2mmErxQ7tbu8kGuszJAq7SQCqywiAyypT+mnRH7L1jZ3xA@mail.gmail.com>
Message-ID: <CALthepz+7+KO1jo5gfiYHtJ-27jojGaHje7D55-B0sHuaZdqYw@mail.gmail.com>

Hi Hannes,

did you try to increase memory settings for your JVM?  e.g. -Xmx500M

Andreas

On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
> <biojava at hannes.oib.com> wrote:
>> Hi again!
>>
>> I am quite happy with the Multiple Sequence Alignment, but I noticed
>> that there seems to be a limit of 132 Sequences that are present in
>> the final alignment - is this some kind of hardcoded limit, or can I
>> work around that somehow?
>>
>> Hannes
>>
>
> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
> fasta format. Is there a way to work around that limit?
>
> Hannes
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From biojava at hannes.oib.com  Wed Oct 19 04:36:19 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 19 Oct 2011 06:36:19 +0200
Subject: [Biojava-l] Multiple Sequence Alignment - Limits?
In-Reply-To: <CALthepz+7+KO1jo5gfiYHtJ-27jojGaHje7D55-B0sHuaZdqYw@mail.gmail.com>
References: <CAPXi2mkLfYxixwx-Wgein7O62ojXm0w-gEdxYfOBBd1KSO-hPA@mail.gmail.com>
	<CAPXi2mmErxQ7tbu8kGuszJAq7SQCqywiAyypT+mnRH7L1jZ3xA@mail.gmail.com>
	<CALthepz+7+KO1jo5gfiYHtJ-27jojGaHje7D55-B0sHuaZdqYw@mail.gmail.com>
Message-ID: <CAPXi2mkBsBJhzfHKtgquytXPV=hF0TZNYAM8cfCcen=QfmAj+A@mail.gmail.com>

Hi Andreas,

I will try that later today if that makes any difference; I ran a
larger alignment batch overnight, and I noticed that this limit seems
to have been a coincidence; HOWEVER, the aligned sequences are always
not as many as the input sequences, is this caused by memory
constraints or how can I influence that?

Hannes

On Tue, Oct 18, 2011 at 23:01, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Hannes,
>
> did you try to increase memory settings for your JVM? ?e.g. -Xmx500M
>
> Andreas
>
> On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandst?tter-M?ller
> <biojava at hannes.oib.com> wrote:
>> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
>> <biojava at hannes.oib.com> wrote:
>>> Hi again!
>>>
>>> I am quite happy with the Multiple Sequence Alignment, but I noticed
>>> that there seems to be a limit of 132 Sequences that are present in
>>> the final alignment - is this some kind of hardcoded limit, or can I
>>> work around that somehow?
>>>
>>> Hannes
>>>
>>
>> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
>> fasta format. Is there a way to work around that limit?
>>
>> Hannes
>>
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>



From biojava at hannes.oib.com  Wed Oct 19 07:32:25 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 19 Oct 2011 09:32:25 +0200
Subject: [Biojava-l] Multiple Sequence Alignment - Limits?
In-Reply-To: <CA+P6arns8F9XeZj4UK0hEmvV_uOG5nJxoZxJ5fBQ=nDh-xuXmg@mail.gmail.com>
References: <CAPXi2mkLfYxixwx-Wgein7O62ojXm0w-gEdxYfOBBd1KSO-hPA@mail.gmail.com>
	<CAPXi2mmErxQ7tbu8kGuszJAq7SQCqywiAyypT+mnRH7L1jZ3xA@mail.gmail.com>
	<CALthepz+7+KO1jo5gfiYHtJ-27jojGaHje7D55-B0sHuaZdqYw@mail.gmail.com>
	<CAPXi2mkBsBJhzfHKtgquytXPV=hF0TZNYAM8cfCcen=QfmAj+A@mail.gmail.com>
	<CA+P6arns8F9XeZj4UK0hEmvV_uOG5nJxoZxJ5fBQ=nDh-xuXmg@mail.gmail.com>
Message-ID: <CAPXi2mnzkvLasRWixinxyh=w=V6bjePXRPhTYGF54ac5dFN57w@mail.gmail.com>

I'm currently running another test, now with even more memory for java
(500M) - it looks fine now so far. I'll re-check it later with the
other files that gave me some problems, and will report back later
today.

I had a "out of heap" exception when I tried it with the default
memory settings, and with 256M it seems to have swallowed some
sequences - I'll re-check and help you reproduce. It would be really
bad if the code would swallow sequences without error messages when
running out of memory, so I'll make sure I have proof :D

Hannes

On Wed, Oct 19, 2011 at 09:22, Spencer Bliven <sbliven at ucsd.edu> wrote:
> Hannes?
>
> There should not be a limit on the number of sequences, nor should you be
> running into a memory problem. The FastaParser should be able to read
> thousands of sequences, since it is used for genome FASTA files as well as
> multiple alignments. My guess would be either a malformed FASTA file
> (perhaps a problem with line endings?), or else a problem with the code to
> generate the MultipleAlignment. Can you post some code snippets?
>
> -Spencer
>
> On Tue, Oct 18, 2011 at 21:36, Hannes Brandst?tter-M?ller
> <biojava at hannes.oib.com> wrote:
>>
>> Hi Andreas,
>>
>> I will try that later today if that makes any difference; I ran a
>> larger alignment batch overnight, and I noticed that this limit seems
>> to have been a coincidence; HOWEVER, the aligned sequences are always
>> not as many as the input sequences, is this caused by memory
>> constraints or how can I influence that?
>>
>> Hannes
>>
>> On Tue, Oct 18, 2011 at 23:01, Andreas Prlic <andreas at sdsc.edu> wrote:
>> > Hi Hannes,
>> >
>> > did you try to increase memory settings for your JVM? ?e.g. -Xmx500M
>> >
>> > Andreas
>> >
>> > On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandst?tter-M?ller
>> > <biojava at hannes.oib.com> wrote:
>> >> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
>> >> <biojava at hannes.oib.com> wrote:
>> >>> Hi again!
>> >>>
>> >>> I am quite happy with the Multiple Sequence Alignment, but I noticed
>> >>> that there seems to be a limit of 132 Sequences that are present in
>> >>> the final alignment - is this some kind of hardcoded limit, or can I
>> >>> work around that somehow?
>> >>>
>> >>> Hannes
>> >>>
>> >>
>> >> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
>> >> fasta format. Is there a way to work around that limit?
>> >>
>> >> Hannes
>> >>
>> >> _______________________________________________
>> >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >>
>> >
>>
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>



From sbliven at ucsd.edu  Wed Oct 19 07:22:55 2011
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Wed, 19 Oct 2011 00:22:55 -0700
Subject: [Biojava-l] Multiple Sequence Alignment - Limits?
In-Reply-To: <CAPXi2mkBsBJhzfHKtgquytXPV=hF0TZNYAM8cfCcen=QfmAj+A@mail.gmail.com>
References: <CAPXi2mkLfYxixwx-Wgein7O62ojXm0w-gEdxYfOBBd1KSO-hPA@mail.gmail.com>
	<CAPXi2mmErxQ7tbu8kGuszJAq7SQCqywiAyypT+mnRH7L1jZ3xA@mail.gmail.com>
	<CALthepz+7+KO1jo5gfiYHtJ-27jojGaHje7D55-B0sHuaZdqYw@mail.gmail.com>
	<CAPXi2mkBsBJhzfHKtgquytXPV=hF0TZNYAM8cfCcen=QfmAj+A@mail.gmail.com>
Message-ID: <CA+P6arns8F9XeZj4UK0hEmvV_uOG5nJxoZxJ5fBQ=nDh-xuXmg@mail.gmail.com>

Hannes?

There should not be a limit on the number of sequences, nor should you be
running into a memory problem. The FastaParser should be able to read
thousands of sequences, since it is used for genome FASTA files as well as
multiple alignments. My guess would be either a malformed FASTA file
(perhaps a problem with line endings?), or else a problem with the code to
generate the MultipleAlignment. Can you post some code snippets?

-Spencer

On Tue, Oct 18, 2011 at 21:36, Hannes Brandst?tter-M?ller <
biojava at hannes.oib.com> wrote:

> Hi Andreas,
>
> I will try that later today if that makes any difference; I ran a
> larger alignment batch overnight, and I noticed that this limit seems
> to have been a coincidence; HOWEVER, the aligned sequences are always
> not as many as the input sequences, is this caused by memory
> constraints or how can I influence that?
>
> Hannes
>
> On Tue, Oct 18, 2011 at 23:01, Andreas Prlic <andreas at sdsc.edu> wrote:
> > Hi Hannes,
> >
> > did you try to increase memory settings for your JVM?  e.g. -Xmx500M
> >
> > Andreas
> >
> > On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandst?tter-M?ller
> > <biojava at hannes.oib.com> wrote:
> >> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
> >> <biojava at hannes.oib.com> wrote:
> >>> Hi again!
> >>>
> >>> I am quite happy with the Multiple Sequence Alignment, but I noticed
> >>> that there seems to be a limit of 132 Sequences that are present in
> >>> the final alignment - is this some kind of hardcoded limit, or can I
> >>> work around that somehow?
> >>>
> >>> Hannes
> >>>
> >>
> >> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
> >> fasta format. Is there a way to work around that limit?
> >>
> >> Hannes
> >>
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>
> >
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From jvb at Cs.Nott.AC.UK  Wed Oct 19 11:15:26 2011
From: jvb at Cs.Nott.AC.UK (jvb at Cs.Nott.AC.UK)
Date: 19 Oct 2011 12:15:26 +0100
Subject: [Biojava-l] Status of org.biojava3.data.sequence.SequenceUtil ?
Message-ID: <201110191215.aa17789@pat.Cs.Nott.AC.UK>

Hello,

I can't find a jar containing org.biojava3.data.sequence.SequenceUtil, even 
though it appears in the JavaDocs: 
http://www.biojava.org/docs/api/org/biojava3/data/sequence/SequenceUtil.html

What is it's status? Can I get it, and should it rely on it if I can?

Thanks,

Jon




From p.v.troshin at dundee.ac.uk  Wed Oct 19 15:13:44 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Wed, 19 Oct 2011 16:13:44 +0100
Subject: [Biojava-l] Status of org.biojava3.data.sequence.SequenceUtil ?
In-Reply-To: <201110191215.aa17789@pat.Cs.Nott.AC.UK>
References: <201110191215.aa17789@pat.Cs.Nott.AC.UK>
Message-ID: <4E9EE928.4050506@dundee.ac.uk>

Hi Jon,

This class is a part of protein disorder prediction JAR and a recent 
addition to BioJava. You are welcome to use if it suits your needs.
Bear in mid though that the FASTA file reader from this class reads the 
content of the whole FASTA file at once, i.e. if you are working with 
large FASTA files you will want to use something else instead. I've got 
a Stream based FASTA reader if you need one and if there is not one in 
BioJava already.
I would imagine the functionality from this class is not going to 
disappear overnight, but it may and perhaps should be merged with other 
FASTA parsers in BioJava once somebody have time to do this.

Regards,
Peter


On 19/10/2011 12:15, jvb at cs.nott.ac.uk wrote:
> Hello,
>
> I can't find a jar containing org.biojava3.data.sequence.SequenceUtil, 
> even though it appears in the JavaDocs: 
> http://www.biojava.org/docs/api/org/biojava3/data/sequence/SequenceUtil.html
>
> What is it's status? Can I get it, and should it rely on it if I can?
>
> Thanks,
>
> Jon
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l



From khalil.elmazouari at gmail.com  Wed Oct 19 18:36:28 2011
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Wed, 19 Oct 2011 20:36:28 +0200
Subject: [Biojava-l] Biojava-l Digest, Vol 105, Issue 12
In-Reply-To: <mailman.3.1319040003.27008.biojava-l@lists.open-bio.org>
References: <mailman.3.1319040003.27008.biojava-l@lists.open-bio.org>
Message-ID: <AA2C5AFF-E988-4EDC-8A2F-86CA67D56BDC@gmail.com>

Hi Hannes,

just did a MSA test with 521 seq... and it works. It must be a memory issue.

try something like: java -Xmx1g -jar yourApp.jar args...

If you don't have enough RAM, try with 500m as suggested by Andreas,

Regards,

Khalil



On 19 Oct 2011, at 18:00, biojava-l-request at lists.open-bio.org wrote:

> Send Biojava-l mailing list submissions to
> 	biojava-l at lists.open-bio.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://lists.open-bio.org/mailman/listinfo/biojava-l
> or, via email, send a message with subject or body 'help' to
> 	biojava-l-request at lists.open-bio.org
> 
> You can reach the person managing the list at
> 	biojava-l-owner at lists.open-bio.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Biojava-l digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: Multiple Sequence Alignment - Limits? (Andreas Prlic)
>   2. Re: Multiple Sequence Alignment - Limits?
>      (Hannes Brandst?tter-M?ller)
>   3. Re: Multiple Sequence Alignment - Limits?
>      (Hannes Brandst?tter-M?ller)
>   4. Re: Multiple Sequence Alignment - Limits? (Spencer Bliven)
>   5. Status of org.biojava3.data.sequence.SequenceUtil ?
>      (jvb at Cs.Nott.AC.UK)
>   6. Re: Status of org.biojava3.data.sequence.SequenceUtil ?
>      (Peter Troshin)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 18 Oct 2011 14:01:05 -0700
> From: Andreas Prlic <andreas at sdsc.edu>
> Subject: Re: [Biojava-l] Multiple Sequence Alignment - Limits?
> To: Hannes Brandst?tter-M?ller <biojava at hannes.oib.com>
> Cc: biojava-l <biojava-l at lists.open-bio.org>
> Message-ID:
> 	<CALthepz+7+KO1jo5gfiYHtJ-27jojGaHje7D55-B0sHuaZdqYw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Hannes,
> 
> did you try to increase memory settings for your JVM?  e.g. -Xmx500M
> 
> Andreas
> 
> On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandst?tter-M?ller
> <biojava at hannes.oib.com> wrote:
>> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
>> <biojava at hannes.oib.com> wrote:
>>> Hi again!
>>> 
>>> I am quite happy with the Multiple Sequence Alignment, but I noticed
>>> that there seems to be a limit of 132 Sequences that are present in
>>> the final alignment - is this some kind of hardcoded limit, or can I
>>> work around that somehow?
>>> 
>>> Hannes
>>> 
>> 
>> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
>> fasta format. Is there a way to work around that limit?
>> 
>> Hannes
>> 
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Wed, 19 Oct 2011 06:36:19 +0200
> From: Hannes Brandst?tter-M?ller 	<biojava at hannes.oib.com>
> Subject: Re: [Biojava-l] Multiple Sequence Alignment - Limits?
> To: Andreas Prlic <andreas at sdsc.edu>
> Cc: biojava-l <biojava-l at lists.open-bio.org>
> Message-ID:
> 	<CAPXi2mkBsBJhzfHKtgquytXPV=hF0TZNYAM8cfCcen=QfmAj+A at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Andreas,
> 
> I will try that later today if that makes any difference; I ran a
> larger alignment batch overnight, and I noticed that this limit seems
> to have been a coincidence; HOWEVER, the aligned sequences are always
> not as many as the input sequences, is this caused by memory
> constraints or how can I influence that?
> 
> Hannes
> 
> On Tue, Oct 18, 2011 at 23:01, Andreas Prlic <andreas at sdsc.edu> wrote:
>> Hi Hannes,
>> 
>> did you try to increase memory settings for your JVM? ?e.g. -Xmx500M
>> 
>> Andreas
>> 
>> On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandst?tter-M?ller
>> <biojava at hannes.oib.com> wrote:
>>> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
>>> <biojava at hannes.oib.com> wrote:
>>>> Hi again!
>>>> 
>>>> I am quite happy with the Multiple Sequence Alignment, but I noticed
>>>> that there seems to be a limit of 132 Sequences that are present in
>>>> the final alignment - is this some kind of hardcoded limit, or can I
>>>> work around that somehow?
>>>> 
>>>> Hannes
>>>> 
>>> 
>>> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
>>> fasta format. Is there a way to work around that limit?
>>> 
>>> Hannes
>>> 
>>> _______________________________________________
>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>> 
>> 
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Wed, 19 Oct 2011 09:32:25 +0200
> From: Hannes Brandst?tter-M?ller 	<biojava at hannes.oib.com>
> Subject: Re: [Biojava-l] Multiple Sequence Alignment - Limits?
> To: Spencer Bliven <sbliven at ucsd.edu>
> Cc: biojava-l <biojava-l at lists.open-bio.org>
> Message-ID:
> 	<CAPXi2mnzkvLasRWixinxyh=w=V6bjePXRPhTYGF54ac5dFN57w at mail.gmail.com>
> Content-Type: text/plain; charset=windows-1252
> 
> I'm currently running another test, now with even more memory for java
> (500M) - it looks fine now so far. I'll re-check it later with the
> other files that gave me some problems, and will report back later
> today.
> 
> I had a "out of heap" exception when I tried it with the default
> memory settings, and with 256M it seems to have swallowed some
> sequences - I'll re-check and help you reproduce. It would be really
> bad if the code would swallow sequences without error messages when
> running out of memory, so I'll make sure I have proof :D
> 
> Hannes
> 
> On Wed, Oct 19, 2011 at 09:22, Spencer Bliven <sbliven at ucsd.edu> wrote:
>> Hannes?
>> 
>> There should not be a limit on the number of sequences, nor should you be
>> running into a memory problem. The FastaParser should be able to read
>> thousands of sequences, since it is used for genome FASTA files as well as
>> multiple alignments. My guess would be either a malformed FASTA file
>> (perhaps a problem with line endings?), or else a problem with the code to
>> generate the MultipleAlignment. Can you post some code snippets?
>> 
>> -Spencer
>> 
>> On Tue, Oct 18, 2011 at 21:36, Hannes Brandst?tter-M?ller
>> <biojava at hannes.oib.com> wrote:
>>> 
>>> Hi Andreas,
>>> 
>>> I will try that later today if that makes any difference; I ran a
>>> larger alignment batch overnight, and I noticed that this limit seems
>>> to have been a coincidence; HOWEVER, the aligned sequences are always
>>> not as many as the input sequences, is this caused by memory
>>> constraints or how can I influence that?
>>> 
>>> Hannes
>>> 
>>> On Tue, Oct 18, 2011 at 23:01, Andreas Prlic <andreas at sdsc.edu> wrote:
>>>> Hi Hannes,
>>>> 
>>>> did you try to increase memory settings for your JVM? ?e.g. -Xmx500M
>>>> 
>>>> Andreas
>>>> 
>>>> On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandst?tter-M?ller
>>>> <biojava at hannes.oib.com> wrote:
>>>>> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
>>>>> <biojava at hannes.oib.com> wrote:
>>>>>> Hi again!
>>>>>> 
>>>>>> I am quite happy with the Multiple Sequence Alignment, but I noticed
>>>>>> that there seems to be a limit of 132 Sequences that are present in
>>>>>> the final alignment - is this some kind of hardcoded limit, or can I
>>>>>> work around that somehow?
>>>>>> 
>>>>>> Hannes
>>>>>> 
>>>>> 
>>>>> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
>>>>> fasta format. Is there a way to work around that limit?
>>>>> 
>>>>> Hannes
>>>>> 
>>>>> _______________________________________________
>>>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>> 
>>>> 
>>> 
>>> _______________________________________________
>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
>> 
> 
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Wed, 19 Oct 2011 00:22:55 -0700
> From: Spencer Bliven <sbliven at ucsd.edu>
> Subject: Re: [Biojava-l] Multiple Sequence Alignment - Limits?
> To: Hannes Brandst?tter-M?ller <biojava at hannes.oib.com>
> Cc: biojava-l <biojava-l at lists.open-bio.org>
> Message-ID:
> 	<CA+P6arns8F9XeZj4UK0hEmvV_uOG5nJxoZxJ5fBQ=nDh-xuXmg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> Hannes?
> 
> There should not be a limit on the number of sequences, nor should you be
> running into a memory problem. The FastaParser should be able to read
> thousands of sequences, since it is used for genome FASTA files as well as
> multiple alignments. My guess would be either a malformed FASTA file
> (perhaps a problem with line endings?), or else a problem with the code to
> generate the MultipleAlignment. Can you post some code snippets?
> 
> -Spencer
> 
> On Tue, Oct 18, 2011 at 21:36, Hannes Brandst?tter-M?ller <
> biojava at hannes.oib.com> wrote:
> 
>> Hi Andreas,
>> 
>> I will try that later today if that makes any difference; I ran a
>> larger alignment batch overnight, and I noticed that this limit seems
>> to have been a coincidence; HOWEVER, the aligned sequences are always
>> not as many as the input sequences, is this caused by memory
>> constraints or how can I influence that?
>> 
>> Hannes
>> 
>> On Tue, Oct 18, 2011 at 23:01, Andreas Prlic <andreas at sdsc.edu> wrote:
>>> Hi Hannes,
>>> 
>>> did you try to increase memory settings for your JVM?  e.g. -Xmx500M
>>> 
>>> Andreas
>>> 
>>> On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandst?tter-M?ller
>>> <biojava at hannes.oib.com> wrote:
>>>> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller
>>>> <biojava at hannes.oib.com> wrote:
>>>>> Hi again!
>>>>> 
>>>>> I am quite happy with the Multiple Sequence Alignment, but I noticed
>>>>> that there seems to be a limit of 132 Sequences that are present in
>>>>> the final alignment - is this some kind of hardcoded limit, or can I
>>>>> work around that somehow?
>>>>> 
>>>>> Hannes
>>>>> 
>>>> 
>>>> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
>>>> fasta format. Is there a way to work around that limit?
>>>> 
>>>> Hannes
>>>> 
>>>> _______________________________________________
>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>> 
>>> 
>> 
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
> 
> 
> 
> ------------------------------
> 
> Message: 5
> Date: 19 Oct 2011 12:15:26 +0100
> From: jvb at Cs.Nott.AC.UK
> Subject: [Biojava-l] Status of org.biojava3.data.sequence.SequenceUtil
> 	?
> To: biojava-l <biojava-l at lists.open-bio.org>
> Message-ID: <201110191215.aa17789 at pat.Cs.Nott.AC.UK>
> Content-Type: text/plain; format=flowed; charset=ISO-8859-1
> 
> Hello,
> 
> I can't find a jar containing org.biojava3.data.sequence.SequenceUtil, even 
> though it appears in the JavaDocs: 
> http://www.biojava.org/docs/api/org/biojava3/data/sequence/SequenceUtil.html
> 
> What is it's status? Can I get it, and should it rely on it if I can?
> 
> Thanks,
> 
> Jon
> 
> 
> 
> 
> ------------------------------
> 
> Message: 6
> Date: Wed, 19 Oct 2011 16:13:44 +0100
> From: Peter Troshin <p.v.troshin at dundee.ac.uk>
> Subject: Re: [Biojava-l] Status of
> 	org.biojava3.data.sequence.SequenceUtil ?
> To: jvb at cs.nott.ac.uk
> Cc: biojava-l at lists.open-bio.org
> Message-ID: <4E9EE928.4050506 at dundee.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi Jon,
> 
> This class is a part of protein disorder prediction JAR and a recent 
> addition to BioJava. You are welcome to use if it suits your needs.
> Bear in mid though that the FASTA file reader from this class reads the 
> content of the whole FASTA file at once, i.e. if you are working with 
> large FASTA files you will want to use something else instead. I've got 
> a Stream based FASTA reader if you need one and if there is not one in 
> BioJava already.
> I would imagine the functionality from this class is not going to 
> disappear overnight, but it may and perhaps should be merged with other 
> FASTA parsers in BioJava once somebody have time to do this.
> 
> Regards,
> Peter
> 
> 
> On 19/10/2011 12:15, jvb at cs.nott.ac.uk wrote:
>> Hello,
>> 
>> I can't find a jar containing org.biojava3.data.sequence.SequenceUtil, 
>> even though it appears in the JavaDocs: 
>> http://www.biojava.org/docs/api/org/biojava3/data/sequence/SequenceUtil.html
>> 
>> What is it's status? Can I get it, and should it rely on it if I can?
>> 
>> Thanks,
>> 
>> Jon
>> 
>> 
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 
> End of Biojava-l Digest, Vol 105, Issue 12
> ******************************************




From biojava at hannes.oib.com  Thu Oct 20 12:29:14 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 20 Oct 2011 14:29:14 +0200
Subject: [Biojava-l] Undeclared/uncaught exception in Fasta Parser
Message-ID: <CAPXi2mngKukzTPS+2PDcUiEY3N3hULuz91BpMtgdOzuRcCgVOQ@mail.gmail.com>

If you feed the fasta parser (code from cookbook) with an empty file, you get a
java.lang.ArrayIndexOutOfBoundsException: 0
        at org.biojava3.core.sequence.io.GenericFastaHeaderParser.parseHeader(GenericFastaHeaderParser.java:111)
        at org.biojava3.core.sequence.io.GenericFastaHeaderParser.parseHeader(GenericFastaHeaderParser.java:60)
        at org.biojava3.core.sequence.io.FastaReader.process(FastaReader.java:136)


Code:

FileInputStream inStream = new FileInputStream(inputFileName);
       FastaReader<DNASequence, NucleotideCompound> fastaReader =
               new FastaReader<DNASequence, NucleotideCompound>(
               inStream,
               new GenericFastaHeaderParser<DNASequence, NucleotideCompound>(),
               new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
       LinkedHashMap<String, DNASequence> originalSeqs =
fastaReader.process(); //boom!

I believe this exception should either be caught and converted to an
IOException or declared.

Hannes

ps: I also ran into an OutOfMemoryError, I tried MSA with approx.
1000+ sequences :D even though I gave java 4000M - are there any
metrics I can use before starting the MSA to determine If it can work?

java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError:
GC overhead limit exceeded
        at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:252)
        at java.util.concurrent.FutureTask.get(FutureTask.java:111)
        at org.biojava3.alignment.Alignments.getProgressiveAlignment(Alignments.java:560)
        at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:187)
        at ...
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
        at java.lang.Integer.valueOf(Integer.java:601)
        at org.biojava3.core.sequence.location.SimplePoint.getPosition(SimplePoint.java:55)
        at org.biojava3.alignment.SimpleAlignedSequence.isGap(SimpleAlignedSequence.java:231)
        at org.biojava3.alignment.SimpleAlignedSequence.getSequenceIndexAt(SimpleAlignedSequence.java:205)
        at org.biojava3.alignment.SimpleAlignedSequence.getCompoundAt(SimpleAlignedSequence.java:270)
        at org.biojava3.alignment.SimpleProfile.getCompoundsAt(SimpleProfile.java:231)
        at org.biojava3.alignment.SimpleProfile.getCompoundCountsAt(SimpleProfile.java:217)
        at org.biojava3.alignment.SimpleProfile.getCompoundWeightsAt(SimpleProfile.java:249)
        at org.biojava3.alignment.template.AbstractProfileProfileAligner.reset(AbstractProfileProfileAligner.java:235)
        at org.biojava3.alignment.template.AbstractProfileProfileAligner.isReady(AbstractProfileProfileAligner.java:215)
        at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:270)
        at org.biojava3.alignment.template.AbstractProfileProfileAligner.getPair(AbstractProfileProfileAligner.java:158)
        at org.biojava3.alignment.template.CallableProfileProfileAligner.call(CallableProfileProfileAligner.java:54)
        at org.biojava3.alignment.template.CallableProfileProfileAligner.call(CallableProfileProfileAligner.java:38)
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
        at java.util.concurrent.FutureTask.run(FutureTask.java:166)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
        at java.lang.Thread.run(Thread.java:636)
java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError:
GC overhead limit exceeded
        at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:252)
        at java.util.concurrent.FutureTask.get(FutureTask.java:111)
        at org.biojava3.alignment.template.AbstractProfileProfileAligner.isReady(AbstractProfileProfileAligner.java:210)
        at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:270)
        at org.biojava3.alignment.template.AbstractProfileProfileAligner.getPair(AbstractProfileProfileAligner.java:158)
        at org.biojava3.alignment.template.CallableProfileProfileAligner.call(CallableProfileProfileAligner.java:54)
        at org.biojava3.alignment.template.CallableProfileProfileAligner.call(CallableProfileProfileAligner.java:38)
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
        at java.util.concurrent.FutureTask.run(FutureTask.java:166)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
        at java.lang.Thread.run(Thread.java:636)
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
        at java.lang.Integer.valueOf(Integer.java:601)
        at org.biojava3.core.sequence.location.SimplePoint.getPosition(SimplePoint.java:55)
        at org.biojava3.alignment.SimpleAlignedSequence.isGap(SimpleAlignedSequence.java:231)
        at org.biojava3.alignment.SimpleAlignedSequence.getSequenceIndexAt(SimpleAlignedSequence.java:205)
        at org.biojava3.alignment.SimpleAlignedSequence.getCompoundAt(SimpleAlignedSequence.java:270)
        at org.biojava3.alignment.SimpleProfile.getCompoundsAt(SimpleProfile.java:231)
        at org.biojava3.alignment.SimpleProfile.getCompoundCountsAt(SimpleProfile.java:217)
        at org.biojava3.alignment.SimpleProfile.getCompoundWeightsAt(SimpleProfile.java:249)
        at org.biojava3.alignment.template.AbstractProfileProfileAligner.reset(AbstractProfileProfileAligner.java:235)
        at org.biojava3.alignment.template.AbstractProfileProfileAligner.isReady(AbstractProfileProfileAligner.java:215)
        ... 9 more


From kern3020 at gmail.com  Thu Oct 20 16:19:27 2011
From: kern3020 at gmail.com (John Kern)
Date: Thu, 20 Oct 2011 09:19:27 -0700
Subject: [Biojava-l]  Multiple Sequence Alignment - Limits?
Message-ID: <CAJ-7iFW=qzwwKLHuzkhp13g0nup4iNsnZTZa9rM6GOVC3Pk_qw@mail.gmail.com>

Hello Hannes,

When programs run out of memory it can be insightful to look at them
via the operating system. It helps to determine if the program
consumes all the memory or is hitting another limit. These comments
are specific to Lunix. All versions of UNIX have similar shells. If
you are running Windows, this is not relevant.

Process size can be limited by a shell on unix systems.

$ man sh
$ ulimit -a
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 20
file size               (blocks, -f) unlimited
pending signals                 (-i) 16382
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) unlimited
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

On my system, there are now limits. What are the results on your system?

If the shell is not limiting your process and as other have pointed
out the JVM isn't limited, the program top can be very insightful.
http://www.kernelhardware.org/linux-top-command/

When the program is running out of memory, does top confirm you have
no more memory?

Regards,
John


From kern3020 at gmail.com  Thu Oct 20 20:12:39 2011
From: kern3020 at gmail.com (John Kern)
Date: Thu, 20 Oct 2011 13:12:39 -0700
Subject: [Biojava-l] demos from 1.8
Message-ID: <CAJ-7iFXugc7rX=4Nc9daufCOh7Y-PxGppnuB8DQAdefNJrLvpw@mail.gmail.com>

Hello,

The 1.8 tutorial refers to a demos directory.
"Additionally, a number of small demo programs can be found in the
demos directory of the BioJava source distribution."

Would it make sense to migrate them to the 3.x APIs?

I downloaded the aggregate tar ball for 1.8.1.  I do not see it there.
Where can I find it?

Thanks,
-john


From andreas at sdsc.edu  Thu Oct 20 21:19:27 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 20 Oct 2011 14:19:27 -0700
Subject: [Biojava-l] demos from 1.8
In-Reply-To: <CAJ-7iFXugc7rX=4Nc9daufCOh7Y-PxGppnuB8DQAdefNJrLvpw@mail.gmail.com>
References: <CAJ-7iFXugc7rX=4Nc9daufCOh7Y-PxGppnuB8DQAdefNJrLvpw@mail.gmail.com>
Message-ID: <CALthepzB89x3twD+-xTQBBaPSbSzzHvY7zvOH0LH6w_BtHdO-A@mail.gmail.com>

Hi John,

several of the 3.X modules have a demo directory that give examples
how to work with them. I believe in the old code base there was also a
demo directory somewhere, not sure if it gets bundled in the aggregate
tar ball though.

Andreas


On Thu, Oct 20, 2011 at 1:12 PM, John Kern <kern3020 at gmail.com> wrote:
> Hello,
>
> The 1.8 tutorial refers to a demos directory.
> "Additionally, a number of small demo programs can be found in the
> demos directory of the BioJava source distribution."
>
> Would it make sense to migrate them to the 3.x APIs?
>
> I downloaded the aggregate tar ball for 1.8.1. ?I do not see it there.
> Where can I find it?
>
> Thanks,
> -john
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From kern3020 at gmail.com  Thu Oct 20 21:33:56 2011
From: kern3020 at gmail.com (John Kern)
Date: Thu, 20 Oct 2011 14:33:56 -0700
Subject: [Biojava-l] demos from 1.8
In-Reply-To: <CALthepzB89x3twD+-xTQBBaPSbSzzHvY7zvOH0LH6w_BtHdO-A@mail.gmail.com>
References: <CAJ-7iFXugc7rX=4Nc9daufCOh7Y-PxGppnuB8DQAdefNJrLvpw@mail.gmail.com>
	<CALthepzB89x3twD+-xTQBBaPSbSzzHvY7zvOH0LH6w_BtHdO-A@mail.gmail.com>
Message-ID: <CAJ-7iFXAK7OxmAyhq5U5qNaaS5UxEak8vuLgUD2Z14RAdFDt1g@mail.gmail.com>

Hello Andreas,

I checked out the 3.x branch from subversion. I see two demo directories.

jkern at ubuntu:~/src/java/biojava-trunk/biojava/biojava3-core/src/main/java/org/biojava3/core/sequence$
find ~/src/java/biojava-trunk/ -name demo
/home/jkern/src/java/biojava-trunk/biojava/biojava3-structure-gui/src/main/java/demo
/home/jkern/src/java/biojava-trunk/biojava/biojava3-structure/src/main/java/demo

I found no corresponding directories in the 1.8.1 tar ball.

One of the articles
(http://biojava.org/wiki/BioJava:Tutorial:Dynamic_programming_examples)
refers to a source file called Dice.java. Would it make sense to
migrate it to the new source? If so, do you know where I can find it?

-jk


On Thu, Oct 20, 2011 at 2:19 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi John,
>
> several of the 3.X modules have a demo directory that give examples
> how to work with them. I believe in the old code base there was also a
> demo directory somewhere, not sure if it gets bundled in the aggregate
> tar ball though.
>
> Andreas
>
>
> On Thu, Oct 20, 2011 at 1:12 PM, John Kern <kern3020 at gmail.com> wrote:
>> Hello,
>>
>> The 1.8 tutorial refers to a demos directory.
>> "Additionally, a number of small demo programs can be found in the
>> demos directory of the BioJava source distribution."
>>
>> Would it make sense to migrate them to the 3.x APIs?
>>
>> I downloaded the aggregate tar ball for 1.8.1. ?I do not see it there.
>> Where can I find it?
>>
>> Thanks,
>> -john
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>



From andreas at sdsc.edu  Thu Oct 20 21:37:44 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 20 Oct 2011 14:37:44 -0700
Subject: [Biojava-l] demos from 1.8
In-Reply-To: <CAJ-7iFXAK7OxmAyhq5U5qNaaS5UxEak8vuLgUD2Z14RAdFDt1g@mail.gmail.com>
References: <CAJ-7iFXugc7rX=4Nc9daufCOh7Y-PxGppnuB8DQAdefNJrLvpw@mail.gmail.com>
	<CALthepzB89x3twD+-xTQBBaPSbSzzHvY7zvOH0LH6w_BtHdO-A@mail.gmail.com>
	<CAJ-7iFXAK7OxmAyhq5U5qNaaS5UxEak8vuLgUD2Z14RAdFDt1g@mail.gmail.com>
Message-ID: <CALthepzEXkb8agfueon_xcUUgq+dYd6PPm-YQfd5NF7M0wNnNw@mail.gmail.com>

I think that most of those demos are heavily dependent on 1.8 code and
would need some major refactoring to work for 3.x. The best reference
to get started is the Cookbook ... (and we probably need more examples
there for 3.X )

Andreas

On Thu, Oct 20, 2011 at 2:33 PM, John Kern <kern3020 at gmail.com> wrote:
> Hello Andreas,
>
> I checked out the 3.x branch from subversion. I see two demo directories.
>
> jkern at ubuntu:~/src/java/biojava-trunk/biojava/biojava3-core/src/main/java/org/biojava3/core/sequence$
> find ~/src/java/biojava-trunk/ -name demo
> /home/jkern/src/java/biojava-trunk/biojava/biojava3-structure-gui/src/main/java/demo
> /home/jkern/src/java/biojava-trunk/biojava/biojava3-structure/src/main/java/demo
>
> I found no corresponding directories in the 1.8.1 tar ball.
>
> One of the articles
> (http://biojava.org/wiki/BioJava:Tutorial:Dynamic_programming_examples)
> refers to a source file called Dice.java. Would it make sense to
> migrate it to the new source? If so, do you know where I can find it?
>
> -jk
>
>
> On Thu, Oct 20, 2011 at 2:19 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> Hi John,
>>
>> several of the 3.X modules have a demo directory that give examples
>> how to work with them. I believe in the old code base there was also a
>> demo directory somewhere, not sure if it gets bundled in the aggregate
>> tar ball though.
>>
>> Andreas
>>
>>
>> On Thu, Oct 20, 2011 at 1:12 PM, John Kern <kern3020 at gmail.com> wrote:
>>> Hello,
>>>
>>> The 1.8 tutorial refers to a demos directory.
>>> "Additionally, a number of small demo programs can be found in the
>>> demos directory of the BioJava source distribution."
>>>
>>> Would it make sense to migrate them to the 3.x APIs?
>>>
>>> I downloaded the aggregate tar ball for 1.8.1. ?I do not see it there.
>>> Where can I find it?
>>>
>>> Thanks,
>>> -john
>>> _______________________________________________
>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>
>



From kern3020 at gmail.com  Wed Oct 26 00:55:39 2011
From: kern3020 at gmail.com (John Kern)
Date: Tue, 25 Oct 2011 17:55:39 -0700
Subject: [Biojava-l] demo directory in API
Message-ID: <CAJ-7iFXjp_HGyz=HQ05igt+xwi__Ld++HUC9d-s54tSjdmkwdg@mail.gmail.com>

Hello,

While reviewing the BioJava 3.x API
(http://www.biojava.org/docs/api/index.html), I noticed the demo
directory Andreas mentioned. I do see it in neither 3.0.2 tarball nor
the subversion checkout from the trunk. If there is a demo directory
for the current source base, I would love to see it.

-jk


From andreas at sdsc.edu  Wed Oct 26 01:00:44 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 25 Oct 2011 18:00:44 -0700
Subject: [Biojava-l] demo directory in API
In-Reply-To: <CAJ-7iFXjp_HGyz=HQ05igt+xwi__Ld++HUC9d-s54tSjdmkwdg@mail.gmail.com>
References: <CAJ-7iFXjp_HGyz=HQ05igt+xwi__Ld++HUC9d-s54tSjdmkwdg@mail.gmail.com>
Message-ID: <CALthepz_rOLmVcXui86aMgsrYO1LC0VDwSQ7r7jSor4pDVerNQ@mail.gmail.com>

it is in the structure module.

Andreas

On Tue, Oct 25, 2011 at 5:55 PM, John Kern <kern3020 at gmail.com> wrote:
> Hello,
>
> While reviewing the BioJava 3.x API
> (http://www.biojava.org/docs/api/index.html), I noticed the demo
> directory Andreas mentioned. I do see it in neither 3.0.2 tarball nor
> the subversion checkout from the trunk. If there is a demo directory
> for the current source base, I would love to see it.
>
> -jk
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From kern3020 at gmail.com  Wed Oct 26 23:00:46 2011
From: kern3020 at gmail.com (John Kern)
Date: Wed, 26 Oct 2011 16:00:46 -0700
Subject: [Biojava-l] What's a good sequence to highlight features in BioJava?
Message-ID: <CAJ-7iFXnoo_LBnPGU3panVJfQz2D=k3WXcHYteXdd8HLJk6OLA@mail.gmail.com>

Hello,

Based I reviewing the 1.8 version of the tutorial, I want to write a
section in the tutorial about features, locations and annotations.
Would someone recommend a good sequence(s) to work with?

Thanks,
-John


From andreas at sdsc.edu  Thu Oct 27 17:44:03 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 27 Oct 2011 10:44:03 -0700
Subject: [Biojava-l] What's a good sequence to highlight features in
	BioJava?
In-Reply-To: <CAJ-7iFXnoo_LBnPGU3panVJfQz2D=k3WXcHYteXdd8HLJk6OLA@mail.gmail.com>
References: <CAJ-7iFXnoo_LBnPGU3panVJfQz2D=k3WXcHYteXdd8HLJk6OLA@mail.gmail.com>
Message-ID: <CALthepzhsVH8JO6q9Wn=fyPxvqhAwFmvjmrf2k4QQg8-+3Eo6w@mail.gmail.com>

Hi John,

Are you working on the 1.8 tutorial? It would be better to focus
documentation efforts on the 3.X branch! We declared the 1.8 code base
to be legacy and all developmental efforts are happening on the 3.X
trunk.

Andreas


On Wed, Oct 26, 2011 at 4:00 PM, John Kern <kern3020 at gmail.com> wrote:
> Hello,
>
> Based I reviewing the 1.8 version of the tutorial, I want to write a
> section in the tutorial about features, locations and annotations.
> Would someone recommend a good sequence(s) to work with?
>
> Thanks,
> -John
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From kern3020 at gmail.com  Thu Oct 27 19:20:54 2011
From: kern3020 at gmail.com (John Kern)
Date: Thu, 27 Oct 2011 12:20:54 -0700
Subject: [Biojava-l] What's a good sequence to highlight features in
	BioJava?
In-Reply-To: <CALthepzhsVH8JO6q9Wn=fyPxvqhAwFmvjmrf2k4QQg8-+3Eo6w@mail.gmail.com>
References: <CAJ-7iFXnoo_LBnPGU3panVJfQz2D=k3WXcHYteXdd8HLJk6OLA@mail.gmail.com>
	<CALthepzhsVH8JO6q9Wn=fyPxvqhAwFmvjmrf2k4QQg8-+3Eo6w@mail.gmail.com>
Message-ID: <CAJ-7iFVLcGEHhD6aygzvUe26zdx-w7a3mK=aGJDxUp3FLb1hEw@mail.gmail.com>

Hello Andreas,

I was still looking at it at a very high level. I want to understand
the appropriate workflow for BioJava. I am a software engineer. I do
not share your background in biology but I want to learn as much as I
possible. I am reading a college-level introduction to biology.
Additional suggestions to my read list would be appreciated.

On Thu, Oct 27, 2011 at 10:44 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Are you working on the 1.8 tutorial? It would be better to focus
> documentation efforts on the 3.X branch! We declared the 1.8 code base
> to be legacy and all developmental efforts are happening on the 3.X
> trunk.

Thanks. I will do that.

Sincerely,
John