From markjschreiber at gmail.com  Fri Dec  1 23:27:16 2006
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Sat, 2 Dec 2006 12:27:16 +0800
Subject: [Biojava-dev] Willing to Contribute in BioJava
In-Reply-To: <BAY114-F251857E4B70C415FFED15ADE60@phx.gbl>
References: <mailman.4952.1164431612.2429.biojava-l@lists.open-bio.org>
	<BAY114-F251857E4B70C415FFED15ADE60@phx.gbl>
Message-ID: <93b45ca50612012027t28154242g540f847649dd6791@mail.gmail.com>

Hi -

There are some areas of the cookbook that need updating to make use of
the new biojava1.5 APIs.

We also need more unit tests for a number of classes.

- Mark

On 11/27/06, Sulaman Nawaz <kingsulaman at hotmail.com> wrote:
>
>
>
>             Subject: Willing to Contribute in BioJava
>
>
>
> Hi everybody I mailed you earlier about biojava contribution, I have gone through API and Cookbook, please help me in identifying how can I help in contributing in this open source  project or Creating any Bio Application using Biojava, I know java programming + XML + Database(SQL)  etc. I want to do as a course project and it could even be extended to Final Program project. I
>
>
>
>
>
>
>
> ..............................
> WITH
> BEST REGARDS
> SULAMAN NAWAZ
>
> E_MAIL:kingsulaman at hotmail.com(primary)
> da_green_berret at yahoo.com(sec.)
> phone +923005096825(mobile)
> +92514580113(res.)
> ________________________________
 Get free, personalized commercial-free online radio with MSN Radio
powered by Pandora
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>
>

From bugzilla-daemon at portal.open-bio.org  Tue Dec  5 22:19:59 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 5 Dec 2006 22:19:59 -0500
Subject: [Biojava-dev] [Bug 2161] New: Feature type string lost after
	RichFeature enrich()
Message-ID: <bug-2161-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2161

           Summary: Feature type string lost after RichFeature enrich()
           Product: BioJava
           Version: unspecified
          Platform: Macintosh
        OS/Version: MacOS X
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: ryan at cs.brown.edu


Version 1.5-beta 

RichFeature.Template t = new RichFeature.Template();
t.type = "my type";
t.location = new PointLocation(1);
Sequence s = DNATools.createDNASequence("A", "my sequence");
Feature f = s.createFeature(t);
System.out.println("f.getType()==" + f.getType()); // prints "my type"
RichFeature rf = RichFeature.Tools.enrich(f);
System.out.println("rf.getType()==" + rf.getType()); // prints "any"


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From bugzilla-daemon at portal.open-bio.org  Tue Dec  5 22:21:03 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 5 Dec 2006 22:21:03 -0500
Subject: [Biojava-dev] [Bug 2161] Feature type string lost after RichFeature
	enrich()
In-Reply-To: <bug-2161-485@http.bugzilla.open-bio.org/>
Message-ID: <200612060321.kB63L3hP020082@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2161





------- Comment #1 from ryan at cs.brown.edu  2006-12-05 22:21 -------
Created an attachment (id=517)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=517&action=view)
Demonstrates bug


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From bugzilla-daemon at portal.open-bio.org  Wed Dec  6 04:47:59 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 6 Dec 2006 04:47:59 -0500
Subject: [Biojava-dev] [Bug 2161] Feature type string lost after RichFeature
	enrich()
In-Reply-To: <bug-2161-485@http.bugzilla.open-bio.org/>
Message-ID: <200612060947.kB69lxmU015549@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2161


holland at ebi.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |INVALID




------- Comment #2 from holland at ebi.ac.uk  2006-12-06 04:47 -------
enrich() uses the typeTerm from the template of the feature to construct the
RichFeature, unless it is null in which case it uses the type instead. In this
case, the typeTerm of the template is "any", and so this is the term that is
used. The assumption is that getType() in RichFeature is just returning the
name of the term returned by getTypeTerm() in the same object. 


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 07:59:10 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 07:59:10 -0500
Subject: [Biojava-dev] [Bug 2164] New: Restriction Mapper - Thread (or dual
	core cpu) problem
Message-ID: <bug-2164-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164

           Summary: Restriction Mapper - Thread (or dual core cpu) problem
           Product: BioJava
           Version: 1.4
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: major
          Priority: P2
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: ilhami.visne at gmail.com


in last summer, i wrote a program, which uses Restriction Mapper. As it was in
example (if i remember correctly), for each enzyme i used one thread. everytime
i got error.

then i noticed, if i use only one enzyme, i get no error. i thought, this could
be a thread-safe issue, because if enzyme count is more than one, more than one
thread will run. therefore i have changed my program to single threaded. and it
has worked well, even for many enzymes. till this week...

one of my clients has run my program on a dual cpu machine. Guess what? Again
same error!!! i have a single-cpu laptop. a friend of mine has a dual-core cpu
laptop. i have tried myself on this machine. And yeah. that is the problem,
because for the same file i don't get any error on my single-core machine, but
everytime the same error on dual-core cpu. Two more important information: 1.
here i got an error for HpaII but it can be any other enzyme. 2. my file has
24000 sequences. the sequence, by which this exception is thrown, is random
too. sometimes the 5600. sequence, another time the 17456. sequence. it changes
too. i checked, all sequences are normal. 

i ran my program today several times, to get the stack trace and i got three
different stack trace. i ran it on my single-core laptop and dual-core laptop.
therefor there are three different stack trace.

1- Exception in thread "Thread-13" org.biojava.bio.BioRuntimeException: Failed
to complete search for HpaII CCGG (1/3)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:137)
        at
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
Caused by: java.lang.NullPointerException
        at
org.biojava.bio.seq.io.SymbolListCharSequence.charAt(SymbolListCharSequence.java:115)
        at java.lang.Character.codePointAt(Unknown Source)
        at java.util.regex.Pattern$Single.match(Unknown Source)
        at java.util.regex.Pattern$Curly.match(Unknown Source)
        at java.util.regex.Pattern$Start.match(Unknown Source)
        at java.util.regex.Matcher.search(Unknown Source)
        at java.util.regex.Matcher.find(Unknown Source)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:104)
        ... 1 more

2- Exception in thread "Thread-2" org.biojava.bio.BioRuntimeException: Failed
to complete search for HpaII CCGG (1/3)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:137)
        at
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
Caused by: java.lang.ArrayIndexOutOfBoundsException
        at java.lang.System.arraycopy(Native Method)
        at java.util.ArrayList.ensureCapacity(Unknown Source)
        at java.util.ArrayList.add(Unknown Source)
        at
org.biojava.bio.seq.SimpleFeatureHolder.addFeature(SimpleFeatureHolder.java:92)
        at
org.biojava.bio.seq.impl.ViewSequence.createFeature(ViewSequence.java:283)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:113)
        ... 1 more

3- Exception in thread "Thread-0" Exception in thread "Thread-1"
org.biojava.bio.BioRuntimeException: Failed to complete search for AluI AGCT
(2/2)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:137)
        at
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 88
        at java.util.ArrayList.add(Unknown Source)
        at
org.biojava.bio.seq.SimpleFeatureHolder.addFeature(SimpleFeatureHolder.java:92)
        at
org.biojava.bio.seq.impl.ViewSequence.createFeature(ViewSequence.java:283)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:113)
        ... 1 more
org.biojava.bio.BioRuntimeException: Failed to complete search for MseI TTAA
(1/3)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:137)
        at
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
Caused by: java.lang.ArrayIndexOutOfBoundsException
        at java.lang.System.arraycopy(Native Method)
        at java.util.ArrayList.ensureCapacity(Unknown Source)
        at java.util.ArrayList.add(Unknown Source)
        at
org.biojava.bio.seq.SimpleFeatureHolder.addFeature(SimpleFeatureHolder.java:92)
        at
org.biojava.bio.seq.impl.ViewSequence.createFeature(ViewSequence.java:283)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:113)
        ... 1 more

Program to use:

//please use a big file. my file has ~24000 sequences. the length of a sequence
doesn't matter
 File sequenceFile = new File("D:/CpG_chr1_plusminus 3000_hg18.fasta");
 BufferedReader br = new BufferedReader(new FileReader(sequenceFile));

 SequenceIterator iter = SeqIOTools.readFastaDNA(br);

 SimpleThreadPool pool = new SimpleThreadPool();

 RestrictionMapper mapper = new RestrictionMapper(pool);

 mapper.addEnzyme(RestrictionEnzymeManager.getEnzyme("MseI"));
 mapper.addEnzyme(RestrictionEnzymeManager.getEnzyme("HpaII"));
 mapper.addEnzyme(RestrictionEnzymeManager.getEnzyme("AluI"));
 Sequence seq;
 while(iter.hasNext()){
     seq = iter.nextSequence();
     mapper.annotate(seq);
 }


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 09:06:05 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 09:06:05 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612131406.kBDE65uO010638@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #1 from jguinney at gmail.com  2006-12-13 09:06 -------
The likely culprit is line 131 in RestrictionSiteFinder:
"target.createFeature(t);"

This is modifying ViewSequence, a class that is NOT thread safe.  Should be
fairly easy to add code that synchronizes on the "target" object.


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 09:21:05 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 09:21:05 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612131421.kBDEL5N3011440@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #2 from jguinney at gmail.com  2006-12-13 09:21 -------

and don't forget line 113 with the same call.

Fix should resemble:
synchronized(target){
  target.createFeature(t);
}


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 09:39:21 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 09:39:21 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612131439.kBDEdLcX012456@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #3 from holland at ebi.ac.uk  2006-12-13 09:39 -------
I have committed a patch as per your suggestions. Please download and compile
the latest version from the head branch of CVS and try it out. If it works or
otherwise don't forget to come back and update this bug report appropriately.


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 15:08:17 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 15:08:17 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612132008.kBDK8HXJ028795@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164


holland at ebi.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED




------- Comment #4 from holland at ebi.ac.uk  2006-12-13 15:08 -------

ON BEHALF OF ORIGINAL POSTER:

i couldn't add a comment in bugzilla. i click commit and wait and wait, 
but nothing happens. what i wanted to add:

I've downloaded and compiled. it still doesn't work. what happens:

1- on my single-core machine, it stops working after 4925. sequence 
every time. It quits from main, but it still runs. probably one or more 
threads are still alive. I've surrounded the code with try/catch in 
main. But it catches no exception and no exception is thrown. At least i 
don't see anything on the monitor.

2- on dual-core machine, this exception is thrown. it doesn't quit too.
Exception in thread "Thread-1" org.biojava.bio.BioRuntimeException: 
Failed to complete search for NarI GGCGCC (2/4)
        at 
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:140)
        at 
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
Caused by: java.lang.NullPointerException
        at 
org.biojava.bio.seq.io.SymbolListCharSequence.charAt(SymbolListCharSequence.java:114)
        at java.lang.Character.codePointAt(Unknown Source)
        at java.util.regex.Pattern$Single.match(Unknown Source)
        at java.util.regex.Pattern$Curly.match(Unknown Source)
        at java.util.regex.Pattern$Start.match(Unknown Source)
        at java.util.regex.Matcher.search(Unknown Source)
        at java.util.regex.Matcher.find(Unknown Source)
        at 
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:103)
        ... 1 more


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 15:09:33 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 15:09:33 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612132009.kBDK9XHO028891@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #5 from holland at ebi.ac.uk  2006-12-13 15:09 -------
OK, I have rolled back the changes I committed earlier as they obviously also
caused single-thread to hang. I have no idea how to proceed though.
Suggestions, anyone?


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 16:53:27 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 16:53:27 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612132153.kBDLrRBC002189@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #6 from jguinney at gmail.com  2006-12-13 16:53 -------
I wouldn't be too hasty to roll back the previous correction.  The problem with
the call to a non-thread safe method stands (and hence the need to synchronize
on 'target'); the ArrayIndexOutOfBoundsException in the call to
SimpleFeatureHolder.addFeature() is highly indicative of this.  

This might suggest other calls to non-thread safe data structures; could be
SymbolListCharSequence since it wraps target (which might explain the null
pointer exception).

(In reply to comment #5)
> OK, I have rolled back the changes I committed earlier as they obviously also
> caused single-thread to hang. I have no idea how to proceed though.
> Suggestions, anyone?
> 


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 16:58:51 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 16:58:51 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612132158.kBDLwpBs002520@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #7 from holland at ebi.ac.uk  2006-12-13 16:58 -------
I figured that by rolling it back, we leave it in the original state when the
bug was first diagnosed. By leaving a patch in place that failed to fix the
bug, we may inadvertently introduce new bugs or mask the original cause. I
prefer to leave the original cause exposed so that whoever comes up with a
solution is not misled by any intervening unsuccesful attempts to fix it. 

Note that I'm not planning on coming up with a solution myself as I have no way
of testing this multi-threaded stuff. :)


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 17:55:30 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 17:55:30 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612132255.kBDMtU9p005646@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #8 from ilhami.visne at gmail.com  2006-12-13 17:55 -------
Some good news. it has hanged on my single-core machine, because i forgot to
call pool.stopThreads(). i am sorry, if i made you do unnecessary efforts
because of it. It works now on my single machine. please roll back the "roll
back" :)

But still  it doesn't work on a dual-core machine. This time a different stack
trace from before. And it may help us to solve this problem

Exception in thread "Thread-0" org.biojava.bio.BioRuntimeException: Failed to
complete search for AluI AGCT (2/2)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:140)
        at
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 444
        at
org.biojava.bio.symbol.PackedSymbolList.symbolAt(PackedSymbolList.java:277)
        at
org.biojava.bio.symbol.ChunkedSymbolList.symbolAt(ChunkedSymbolList.java:91)
        at
org.biojavax.bio.seq.DummyRichSequenceHandler.symbolAt(DummyRichSequenceHandler.java:39)
        at
org.biojavax.bio.seq.ThinRichSequence.symbolAt(ThinRichSequence.java:163)
        at
org.biojava.bio.seq.impl.ViewSequence.symbolAt(ViewSequence.java:185)

        at
org.biojava.bio.seq.io.SymbolListCharSequence.charAt(SymbolListCharSequence.java:114)
        at java.util.regex.Pattern$BnM.match(Unknown Source)
        at java.util.regex.Matcher.search(Unknown Source)
        at java.util.regex.Matcher.find(Unknown Source)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:103)
        ... 1 more

As you see, it is an java.lang.ArrayIndexOutOfBoundsException: 444.
None of my sequences is smaller than 5000 bases. How can the index 444 cause
this exception???


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 20:00:20 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 20:00:20 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612140100.kBE10Kbi012245@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #9 from jguinney at gmail.com  2006-12-13 20:00 -------
Here are the comments at the top of org.biojava.bio.symbol.PackedSymbolList,
and I quote:

"WARNING: these variables constitute an opportunity
for things to go wrong when doing multithreaded access
via symbolAt().  Keep SymbolAt() synchronized so they
don't get changed during a lookup! Naaasssty."


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From markjschreiber at gmail.com  Mon Dec 18 21:59:00 2006
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Tue, 19 Dec 2006 10:59:00 +0800
Subject: [Biojava-dev] Message to developers with CVS accounts
Message-ID: <93b45ca50612181859v7a1fc678jb15b2a4967a3353c@mail.gmail.com>

Dear all -

When committing to CVS please don't include the following files and
directories:

.cvsignore
nbproject/
reports/
dist/
docs/
ant-build/

These files are generated on your machine by ant and by the netbeans IDE.
They don't need to be in CVS and can cause all kinds of conflicts when they
are. They are most frequently checked in by IDEs that support CVS (esp
Netbeans). If Netbeans tells you you need to check in one of these files
cause it is new tell it to ignore them. They will be added to your
.cvsignore and ignored in future. Remember your .cvsignore is specific to
your distribution and doesn't need to be in CVS either and could cause a
conflict if you check it in.

Don't do it!!

- Mark

From markjschreiber at gmail.com  Mon Dec 18 22:02:53 2006
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Tue, 19 Dec 2006 11:02:53 +0800
Subject: [Biojava-dev] Message to developers with CVS accounts
Message-ID: <93b45ca50612181902n11196408wa891dbcd13788100@mail.gmail.com>

Dear all -

When committing to CVS please don't include the following files and directories:

.cvsignore
nbproject/
reports/
dist/
docs/
ant-build/

These files are generated on your machine by ant and by the netbeans
IDE. They don't need to be in CVS and can cause all kinds of conflicts
when they are. They are most frequently checked in by IDEs that
support CVS (esp Netbeans). If Netbeans tells you you need to check in
one of these files cause it is new tell it to ignore them. They will
be added to your .cvsignore and ignored in future. Remember your
.cvsignore is specific to your distribution and doesn't need to be in
CVS either and could cause a conflict if you check it in.

Don't do it!!

- Mark

From tamir at imp.univie.ac.at  Wed Dec 20 10:58:02 2006
From: tamir at imp.univie.ac.at (Ido M. Tamir)
Date: Wed, 20 Dec 2006 16:58:02 +0100
Subject: [Biojava-dev] SimpleGFFRecord
Message-ID: <200612201658.02312.tamir@imp.univie.ac.at>

Hi,
SimpleGFFRecord puts out one additional semicolon
at the end of the attributes. Shifting sBuff.append(";")
to the test changes that.

old:

 public static String stringifyAttributes(Map attMap) {
    StringBuffer sBuff = new StringBuffer();
    Iterator ki = attMap.keySet().iterator();
    while (ki.hasNext()) {
      String key = (String) ki.next();
      sBuff.append(key);
      List values = (List) attMap.get(key);
      for (Iterator vi = values.iterator(); vi.hasNext();) {
        String value = (String) vi.next();
        if (isText(value)) {
          sBuff.append(" \"" + value + "\"");
        } else {
          sBuff.append(" " + value);
        }
      }
      sBuff.append(";");            <---!!
      if (ki.hasNext()) {
        sBuff.append(" ");
      }
    }
    return sBuff.substring(0);
  }


 public static String stringifyAttributes(Map attMap) {
    StringBuffer sBuff = new StringBuffer();
    Iterator ki = attMap.keySet().iterator();
    while (ki.hasNext()) {
      String key = (String) ki.next();
      sBuff.append(key);
      List values = (List) attMap.get(key);
      for (Iterator vi = values.iterator(); vi.hasNext();) {
        String value = (String) vi.next();
        if (isText(value)) {
          sBuff.append(" \"" + value + "\"");
        } else {
          sBuff.append(" " + value);
        }
      }
      if (ki.hasNext()) {
 	sBuff.append(";");           <---!!
        sBuff.append(" ");
      }
    }
    return sBuff.substring(0);
  }

From bugzilla-daemon at portal.open-bio.org  Thu Dec 28 22:34:00 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 28 Dec 2006 22:34:00 -0500
Subject: [Biojava-dev] [Bug 2171] New: UniProt format cannot read ID line
Message-ID: <bug-2171-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2171

           Summary: UniProt format cannot read ID line
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: critical
          Priority: P1
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: mark.schreiber at novartis.com


Possibly the UniProt format has changed but the Pattern in UniProtFormat.java
at line 125 no longer matches the ID lines of UniProt files.

eg:

ID   POLG_DEN1S              Reviewed;        3396 AA.
AC   P33478;
DT   01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1994, sequence version 1.
DT   12-DEC-2006, entry version 62.
etc...


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From bugzilla-daemon at portal.open-bio.org  Fri Dec 29 00:32:43 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 29 Dec 2006 00:32:43 -0500
Subject: [Biojava-dev] [Bug 2171] UniProt format cannot read ID line
In-Reply-To: <bug-2171-485@http.bugzilla.open-bio.org/>
Message-ID: <200612290532.kBT5WhiS016157@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2171


mark.schreiber at novartis.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




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From markjschreiber at gmail.com  Sat Dec  2 04:27:16 2006
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Sat, 2 Dec 2006 12:27:16 +0800
Subject: [Biojava-dev] Willing to Contribute in BioJava
In-Reply-To: <BAY114-F251857E4B70C415FFED15ADE60@phx.gbl>
References: <mailman.4952.1164431612.2429.biojava-l@lists.open-bio.org>
	<BAY114-F251857E4B70C415FFED15ADE60@phx.gbl>
Message-ID: <93b45ca50612012027t28154242g540f847649dd6791@mail.gmail.com>

Hi -

There are some areas of the cookbook that need updating to make use of
the new biojava1.5 APIs.

We also need more unit tests for a number of classes.

- Mark

On 11/27/06, Sulaman Nawaz <kingsulaman at hotmail.com> wrote:
>
>
>
>             Subject: Willing to Contribute in BioJava
>
>
>
> Hi everybody I mailed you earlier about biojava contribution, I have gone through API and Cookbook, please help me in identifying how can I help in contributing in this open source  project or Creating any Bio Application using Biojava, I know java programming + XML + Database(SQL)  etc. I want to do as a course project and it could even be extended to Final Program project. I
>
>
>
>
>
>
>
> ..............................
> WITH
> BEST REGARDS
> SULAMAN NAWAZ
>
> E_MAIL:kingsulaman at hotmail.com(primary)
> da_green_berret at yahoo.com(sec.)
> phone +923005096825(mobile)
> +92514580113(res.)
> ________________________________
 Get free, personalized commercial-free online radio with MSN Radio
powered by Pandora
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>
>


From bugzilla-daemon at portal.open-bio.org  Wed Dec  6 03:19:59 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 5 Dec 2006 22:19:59 -0500
Subject: [Biojava-dev] [Bug 2161] New: Feature type string lost after
	RichFeature enrich()
Message-ID: <bug-2161-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2161

           Summary: Feature type string lost after RichFeature enrich()
           Product: BioJava
           Version: unspecified
          Platform: Macintosh
        OS/Version: MacOS X
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: ryan at cs.brown.edu


Version 1.5-beta 

RichFeature.Template t = new RichFeature.Template();
t.type = "my type";
t.location = new PointLocation(1);
Sequence s = DNATools.createDNASequence("A", "my sequence");
Feature f = s.createFeature(t);
System.out.println("f.getType()==" + f.getType()); // prints "my type"
RichFeature rf = RichFeature.Tools.enrich(f);
System.out.println("rf.getType()==" + rf.getType()); // prints "any"


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From bugzilla-daemon at portal.open-bio.org  Wed Dec  6 03:21:03 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 5 Dec 2006 22:21:03 -0500
Subject: [Biojava-dev] [Bug 2161] Feature type string lost after RichFeature
	enrich()
In-Reply-To: <bug-2161-485@http.bugzilla.open-bio.org/>
Message-ID: <200612060321.kB63L3hP020082@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2161





------- Comment #1 from ryan at cs.brown.edu  2006-12-05 22:21 -------
Created an attachment (id=517)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=517&action=view)
Demonstrates bug


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From bugzilla-daemon at portal.open-bio.org  Wed Dec  6 09:47:59 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 6 Dec 2006 04:47:59 -0500
Subject: [Biojava-dev] [Bug 2161] Feature type string lost after RichFeature
	enrich()
In-Reply-To: <bug-2161-485@http.bugzilla.open-bio.org/>
Message-ID: <200612060947.kB69lxmU015549@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2161


holland at ebi.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |INVALID




------- Comment #2 from holland at ebi.ac.uk  2006-12-06 04:47 -------
enrich() uses the typeTerm from the template of the feature to construct the
RichFeature, unless it is null in which case it uses the type instead. In this
case, the typeTerm of the template is "any", and so this is the term that is
used. The assumption is that getType() in RichFeature is just returning the
name of the term returned by getTypeTerm() in the same object. 


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 12:59:10 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 07:59:10 -0500
Subject: [Biojava-dev] [Bug 2164] New: Restriction Mapper - Thread (or dual
	core cpu) problem
Message-ID: <bug-2164-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164

           Summary: Restriction Mapper - Thread (or dual core cpu) problem
           Product: BioJava
           Version: 1.4
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: major
          Priority: P2
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: ilhami.visne at gmail.com


in last summer, i wrote a program, which uses Restriction Mapper. As it was in
example (if i remember correctly), for each enzyme i used one thread. everytime
i got error.

then i noticed, if i use only one enzyme, i get no error. i thought, this could
be a thread-safe issue, because if enzyme count is more than one, more than one
thread will run. therefore i have changed my program to single threaded. and it
has worked well, even for many enzymes. till this week...

one of my clients has run my program on a dual cpu machine. Guess what? Again
same error!!! i have a single-cpu laptop. a friend of mine has a dual-core cpu
laptop. i have tried myself on this machine. And yeah. that is the problem,
because for the same file i don't get any error on my single-core machine, but
everytime the same error on dual-core cpu. Two more important information: 1.
here i got an error for HpaII but it can be any other enzyme. 2. my file has
24000 sequences. the sequence, by which this exception is thrown, is random
too. sometimes the 5600. sequence, another time the 17456. sequence. it changes
too. i checked, all sequences are normal. 

i ran my program today several times, to get the stack trace and i got three
different stack trace. i ran it on my single-core laptop and dual-core laptop.
therefor there are three different stack trace.

1- Exception in thread "Thread-13" org.biojava.bio.BioRuntimeException: Failed
to complete search for HpaII CCGG (1/3)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:137)
        at
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
Caused by: java.lang.NullPointerException
        at
org.biojava.bio.seq.io.SymbolListCharSequence.charAt(SymbolListCharSequence.java:115)
        at java.lang.Character.codePointAt(Unknown Source)
        at java.util.regex.Pattern$Single.match(Unknown Source)
        at java.util.regex.Pattern$Curly.match(Unknown Source)
        at java.util.regex.Pattern$Start.match(Unknown Source)
        at java.util.regex.Matcher.search(Unknown Source)
        at java.util.regex.Matcher.find(Unknown Source)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:104)
        ... 1 more

2- Exception in thread "Thread-2" org.biojava.bio.BioRuntimeException: Failed
to complete search for HpaII CCGG (1/3)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:137)
        at
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
Caused by: java.lang.ArrayIndexOutOfBoundsException
        at java.lang.System.arraycopy(Native Method)
        at java.util.ArrayList.ensureCapacity(Unknown Source)
        at java.util.ArrayList.add(Unknown Source)
        at
org.biojava.bio.seq.SimpleFeatureHolder.addFeature(SimpleFeatureHolder.java:92)
        at
org.biojava.bio.seq.impl.ViewSequence.createFeature(ViewSequence.java:283)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:113)
        ... 1 more

3- Exception in thread "Thread-0" Exception in thread "Thread-1"
org.biojava.bio.BioRuntimeException: Failed to complete search for AluI AGCT
(2/2)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:137)
        at
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 88
        at java.util.ArrayList.add(Unknown Source)
        at
org.biojava.bio.seq.SimpleFeatureHolder.addFeature(SimpleFeatureHolder.java:92)
        at
org.biojava.bio.seq.impl.ViewSequence.createFeature(ViewSequence.java:283)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:113)
        ... 1 more
org.biojava.bio.BioRuntimeException: Failed to complete search for MseI TTAA
(1/3)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:137)
        at
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
Caused by: java.lang.ArrayIndexOutOfBoundsException
        at java.lang.System.arraycopy(Native Method)
        at java.util.ArrayList.ensureCapacity(Unknown Source)
        at java.util.ArrayList.add(Unknown Source)
        at
org.biojava.bio.seq.SimpleFeatureHolder.addFeature(SimpleFeatureHolder.java:92)
        at
org.biojava.bio.seq.impl.ViewSequence.createFeature(ViewSequence.java:283)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:113)
        ... 1 more

Program to use:

//please use a big file. my file has ~24000 sequences. the length of a sequence
doesn't matter
 File sequenceFile = new File("D:/CpG_chr1_plusminus 3000_hg18.fasta");
 BufferedReader br = new BufferedReader(new FileReader(sequenceFile));

 SequenceIterator iter = SeqIOTools.readFastaDNA(br);

 SimpleThreadPool pool = new SimpleThreadPool();

 RestrictionMapper mapper = new RestrictionMapper(pool);

 mapper.addEnzyme(RestrictionEnzymeManager.getEnzyme("MseI"));
 mapper.addEnzyme(RestrictionEnzymeManager.getEnzyme("HpaII"));
 mapper.addEnzyme(RestrictionEnzymeManager.getEnzyme("AluI"));
 Sequence seq;
 while(iter.hasNext()){
     seq = iter.nextSequence();
     mapper.annotate(seq);
 }


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 14:06:05 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 09:06:05 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612131406.kBDE65uO010638@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #1 from jguinney at gmail.com  2006-12-13 09:06 -------
The likely culprit is line 131 in RestrictionSiteFinder:
"target.createFeature(t);"

This is modifying ViewSequence, a class that is NOT thread safe.  Should be
fairly easy to add code that synchronizes on the "target" object.


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 14:21:05 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 09:21:05 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612131421.kBDEL5N3011440@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #2 from jguinney at gmail.com  2006-12-13 09:21 -------

and don't forget line 113 with the same call.

Fix should resemble:
synchronized(target){
  target.createFeature(t);
}


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 14:39:21 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 09:39:21 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612131439.kBDEdLcX012456@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #3 from holland at ebi.ac.uk  2006-12-13 09:39 -------
I have committed a patch as per your suggestions. Please download and compile
the latest version from the head branch of CVS and try it out. If it works or
otherwise don't forget to come back and update this bug report appropriately.


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 20:08:17 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 15:08:17 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612132008.kBDK8HXJ028795@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164


holland at ebi.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED




------- Comment #4 from holland at ebi.ac.uk  2006-12-13 15:08 -------

ON BEHALF OF ORIGINAL POSTER:

i couldn't add a comment in bugzilla. i click commit and wait and wait, 
but nothing happens. what i wanted to add:

I've downloaded and compiled. it still doesn't work. what happens:

1- on my single-core machine, it stops working after 4925. sequence 
every time. It quits from main, but it still runs. probably one or more 
threads are still alive. I've surrounded the code with try/catch in 
main. But it catches no exception and no exception is thrown. At least i 
don't see anything on the monitor.

2- on dual-core machine, this exception is thrown. it doesn't quit too.
Exception in thread "Thread-1" org.biojava.bio.BioRuntimeException: 
Failed to complete search for NarI GGCGCC (2/4)
        at 
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:140)
        at 
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
Caused by: java.lang.NullPointerException
        at 
org.biojava.bio.seq.io.SymbolListCharSequence.charAt(SymbolListCharSequence.java:114)
        at java.lang.Character.codePointAt(Unknown Source)
        at java.util.regex.Pattern$Single.match(Unknown Source)
        at java.util.regex.Pattern$Curly.match(Unknown Source)
        at java.util.regex.Pattern$Start.match(Unknown Source)
        at java.util.regex.Matcher.search(Unknown Source)
        at java.util.regex.Matcher.find(Unknown Source)
        at 
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:103)
        ... 1 more


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 20:09:33 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 15:09:33 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612132009.kBDK9XHO028891@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #5 from holland at ebi.ac.uk  2006-12-13 15:09 -------
OK, I have rolled back the changes I committed earlier as they obviously also
caused single-thread to hang. I have no idea how to proceed though.
Suggestions, anyone?


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 21:53:27 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 16:53:27 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612132153.kBDLrRBC002189@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #6 from jguinney at gmail.com  2006-12-13 16:53 -------
I wouldn't be too hasty to roll back the previous correction.  The problem with
the call to a non-thread safe method stands (and hence the need to synchronize
on 'target'); the ArrayIndexOutOfBoundsException in the call to
SimpleFeatureHolder.addFeature() is highly indicative of this.  

This might suggest other calls to non-thread safe data structures; could be
SymbolListCharSequence since it wraps target (which might explain the null
pointer exception).

(In reply to comment #5)
> OK, I have rolled back the changes I committed earlier as they obviously also
> caused single-thread to hang. I have no idea how to proceed though.
> Suggestions, anyone?
> 


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 21:58:51 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 16:58:51 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612132158.kBDLwpBs002520@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #7 from holland at ebi.ac.uk  2006-12-13 16:58 -------
I figured that by rolling it back, we leave it in the original state when the
bug was first diagnosed. By leaving a patch in place that failed to fix the
bug, we may inadvertently introduce new bugs or mask the original cause. I
prefer to leave the original cause exposed so that whoever comes up with a
solution is not misled by any intervening unsuccesful attempts to fix it. 

Note that I'm not planning on coming up with a solution myself as I have no way
of testing this multi-threaded stuff. :)


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From bugzilla-daemon at portal.open-bio.org  Wed Dec 13 22:55:30 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 17:55:30 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612132255.kBDMtU9p005646@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #8 from ilhami.visne at gmail.com  2006-12-13 17:55 -------
Some good news. it has hanged on my single-core machine, because i forgot to
call pool.stopThreads(). i am sorry, if i made you do unnecessary efforts
because of it. It works now on my single machine. please roll back the "roll
back" :)

But still  it doesn't work on a dual-core machine. This time a different stack
trace from before. And it may help us to solve this problem

Exception in thread "Thread-0" org.biojava.bio.BioRuntimeException: Failed to
complete search for AluI AGCT (2/2)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:140)
        at
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 444
        at
org.biojava.bio.symbol.PackedSymbolList.symbolAt(PackedSymbolList.java:277)
        at
org.biojava.bio.symbol.ChunkedSymbolList.symbolAt(ChunkedSymbolList.java:91)
        at
org.biojavax.bio.seq.DummyRichSequenceHandler.symbolAt(DummyRichSequenceHandler.java:39)
        at
org.biojavax.bio.seq.ThinRichSequence.symbolAt(ThinRichSequence.java:163)
        at
org.biojava.bio.seq.impl.ViewSequence.symbolAt(ViewSequence.java:185)

        at
org.biojava.bio.seq.io.SymbolListCharSequence.charAt(SymbolListCharSequence.java:114)
        at java.util.regex.Pattern$BnM.match(Unknown Source)
        at java.util.regex.Matcher.search(Unknown Source)
        at java.util.regex.Matcher.find(Unknown Source)
        at
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:103)
        ... 1 more

As you see, it is an java.lang.ArrayIndexOutOfBoundsException: 444.
None of my sequences is smaller than 5000 bases. How can the index 444 cause
this exception???


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From bugzilla-daemon at portal.open-bio.org  Thu Dec 14 01:00:20 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 13 Dec 2006 20:00:20 -0500
Subject: [Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core
	cpu) problem
In-Reply-To: <bug-2164-485@http.bugzilla.open-bio.org/>
Message-ID: <200612140100.kBE10Kbi012245@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #9 from jguinney at gmail.com  2006-12-13 20:00 -------
Here are the comments at the top of org.biojava.bio.symbol.PackedSymbolList,
and I quote:

"WARNING: these variables constitute an opportunity
for things to go wrong when doing multithreaded access
via symbolAt().  Keep SymbolAt() synchronized so they
don't get changed during a lookup! Naaasssty."


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From markjschreiber at gmail.com  Tue Dec 19 02:59:00 2006
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Tue, 19 Dec 2006 10:59:00 +0800
Subject: [Biojava-dev] Message to developers with CVS accounts
Message-ID: <93b45ca50612181859v7a1fc678jb15b2a4967a3353c@mail.gmail.com>

Dear all -

When committing to CVS please don't include the following files and
directories:

.cvsignore
nbproject/
reports/
dist/
docs/
ant-build/

These files are generated on your machine by ant and by the netbeans IDE.
They don't need to be in CVS and can cause all kinds of conflicts when they
are. They are most frequently checked in by IDEs that support CVS (esp
Netbeans). If Netbeans tells you you need to check in one of these files
cause it is new tell it to ignore them. They will be added to your
.cvsignore and ignored in future. Remember your .cvsignore is specific to
your distribution and doesn't need to be in CVS either and could cause a
conflict if you check it in.

Don't do it!!

- Mark


From markjschreiber at gmail.com  Tue Dec 19 03:02:53 2006
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Tue, 19 Dec 2006 11:02:53 +0800
Subject: [Biojava-dev] Message to developers with CVS accounts
Message-ID: <93b45ca50612181902n11196408wa891dbcd13788100@mail.gmail.com>

Dear all -

When committing to CVS please don't include the following files and directories:

.cvsignore
nbproject/
reports/
dist/
docs/
ant-build/

These files are generated on your machine by ant and by the netbeans
IDE. They don't need to be in CVS and can cause all kinds of conflicts
when they are. They are most frequently checked in by IDEs that
support CVS (esp Netbeans). If Netbeans tells you you need to check in
one of these files cause it is new tell it to ignore them. They will
be added to your .cvsignore and ignored in future. Remember your
.cvsignore is specific to your distribution and doesn't need to be in
CVS either and could cause a conflict if you check it in.

Don't do it!!

- Mark


From tamir at imp.univie.ac.at  Wed Dec 20 15:58:02 2006
From: tamir at imp.univie.ac.at (Ido M. Tamir)
Date: Wed, 20 Dec 2006 16:58:02 +0100
Subject: [Biojava-dev] SimpleGFFRecord
Message-ID: <200612201658.02312.tamir@imp.univie.ac.at>

Hi,
SimpleGFFRecord puts out one additional semicolon
at the end of the attributes. Shifting sBuff.append(";")
to the test changes that.

old:

 public static String stringifyAttributes(Map attMap) {
    StringBuffer sBuff = new StringBuffer();
    Iterator ki = attMap.keySet().iterator();
    while (ki.hasNext()) {
      String key = (String) ki.next();
      sBuff.append(key);
      List values = (List) attMap.get(key);
      for (Iterator vi = values.iterator(); vi.hasNext();) {
        String value = (String) vi.next();
        if (isText(value)) {
          sBuff.append(" \"" + value + "\"");
        } else {
          sBuff.append(" " + value);
        }
      }
      sBuff.append(";");            <---!!
      if (ki.hasNext()) {
        sBuff.append(" ");
      }
    }
    return sBuff.substring(0);
  }


 public static String stringifyAttributes(Map attMap) {
    StringBuffer sBuff = new StringBuffer();
    Iterator ki = attMap.keySet().iterator();
    while (ki.hasNext()) {
      String key = (String) ki.next();
      sBuff.append(key);
      List values = (List) attMap.get(key);
      for (Iterator vi = values.iterator(); vi.hasNext();) {
        String value = (String) vi.next();
        if (isText(value)) {
          sBuff.append(" \"" + value + "\"");
        } else {
          sBuff.append(" " + value);
        }
      }
      if (ki.hasNext()) {
 	sBuff.append(";");           <---!!
        sBuff.append(" ");
      }
    }
    return sBuff.substring(0);
  }


From bugzilla-daemon at portal.open-bio.org  Fri Dec 29 03:34:00 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 28 Dec 2006 22:34:00 -0500
Subject: [Biojava-dev] [Bug 2171] New: UniProt format cannot read ID line
Message-ID: <bug-2171-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2171

           Summary: UniProt format cannot read ID line
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: critical
          Priority: P1
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: mark.schreiber at novartis.com


Possibly the UniProt format has changed but the Pattern in UniProtFormat.java
at line 125 no longer matches the ID lines of UniProt files.

eg:

ID   POLG_DEN1S              Reviewed;        3396 AA.
AC   P33478;
DT   01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1994, sequence version 1.
DT   12-DEC-2006, entry version 62.
etc...


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From bugzilla-daemon at portal.open-bio.org  Fri Dec 29 05:32:43 2006
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 29 Dec 2006 00:32:43 -0500
Subject: [Biojava-dev] [Bug 2171] UniProt format cannot read ID line
In-Reply-To: <bug-2171-485@http.bugzilla.open-bio.org/>
Message-ID: <200612290532.kBT5WhiS016157@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2171


mark.schreiber at novartis.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




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