From zbhuang2005 at hotmail.com  Tue Jan  2 08:16:16 2007
From: zbhuang2005 at hotmail.com (Huang Zhibin)
Date: Tue, 02 Jan 2007 13:16:16 +0000
Subject: [Biojava-dev] how to run unittest in eclipse
Message-ID: <BAY7-F23C6E75109962FA246420CA5BA0@phx.gbl>

Dear all,
  First all,thanks for the contribution of BioJava.
  I downloaded the BioJava and compile apps, demos, tests and runtests 
using ant. It is ok. But when importing this project into eclipse, I do not 
know hot to runtests. For example, when clicking file of 
/tests/org.biojava.bio.alignment/FlexibleAlignmentTest.java, choose Run As 
| JUnit Test, it fails. Info in Console will be listed below.
  I know maybe it failed in the step of initialization, but I do now know 
how to solve it.
  Can someone who run junittest in JAVA IDE share the experience or give me 
some suggestions? I will appreciate it.
Best regards,
Zhibin

------------------------------
Info printed in Console:

org.biojava.bio.BioError: Unable to initialize DNATools
	at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:117)
	at 
org.biojava.bio.alignment.FlexibleAlignmentTest.parse(FlexibleAlignmentTest.java:74)

	at 
org.biojava.bio.alignment.FlexibleAlignmentTest.<clinit>(FlexibleAlignmentTest.java:46)

	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown 
Source)
	at java.lang.reflect.Constructor.newInstance(Unknown Source)
	at junit.framework.TestSuite.createTest(TestSuite.java:135)
	at junit.framework.TestSuite.addTestMethod(TestSuite.java:114)
	at junit.framework.TestSuite.<init>(TestSuite.java:75)
	at 
org.eclipse.jdt.internal.junit.runner.junit3.JUnit3TestLoader.getTest(JUnit3TestLoader.java:102)

	at 
org.eclipse.jdt.internal.junit.runner.junit3.JUnit3TestLoader.loadTests(JUnit3TestLoader.java:59)

	at 
org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:445)

	at 
org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:673)

	at 
org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:386)

	at 
org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:196)

Caused by: org.biojava.bio.BioError: Couldn't locate AlphabetManager.xml.  
This probably means that your biojava.jar file is corrupt or incorrectly 
built.
	at 
org.biojava.bio.symbol.AlphabetManager.<clinit>(AlphabetManager.java:148)
	at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:80)
	... 15 more
java.lang.NoClassDefFoundError
	at org.biojava.bio.seq.ProteinTools.<clinit>(ProteinTools.java:76)
	at 
org.biojava.bio.alignment.FlexibleAlignmentTest.parse(FlexibleAlignmentTest.java:76)


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From bugzilla-daemon at portal.open-bio.org  Wed Jan  3 11:55:12 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 3 Jan 2007 11:55:12 -0500
Subject: [Biojava-dev] [Bug 2175] New: IndexOutOfBoundsException still
	occurring on SCF.create(File file)
Message-ID: <bug-2175-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2175

           Summary: IndexOutOfBoundsException still occurring on
                    SCF.create(File file)
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: blocker
          Priority: P1
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: cristyn at broad.mit.edu


SCF.create(File file) is still broken. I'm using the 1.5-beta2 download. Here
is the stacktrace:

ava.lang.IndexOutOfBoundsException
        at java.io.FileInputStream.readBytes(Native Method)
        at java.io.FileInputStream.read(FileInputStream.java:199)
        at java.io.DataInputStream.read(DataInputStream.java:132)
        at org.biojava.bio.program.scf.SCF$Parser.parsePrivate(SCF.java:391)
        at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:349)
        at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:202)
        at org.biojava.bio.program.scf.SCF.load(SCF.java:145)
        at org.biojava.bio.program.scf.SCF.load(SCF.java:140)
        at org.biojava.bio.program.scf.SCF.create(SCF.java:126)


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From bugzilla-daemon at portal.open-bio.org  Wed Jan  3 11:56:15 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 3 Jan 2007 11:56:15 -0500
Subject: [Biojava-dev] [Bug 2175] IndexOutOfBoundsException still occurring
	on SCF.create(File file)
In-Reply-To: <bug-2175-485@http.bugzilla.open-bio.org/>
Message-ID: <200701031656.l03GuFcn015619@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2175


cristyn at broad.mit.edu changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |cristyn at broad.mit.edu




------- Comment #1 from cristyn at broad.mit.edu  2007-01-03 11:56 -------
java.lang.IndexOutOfBoundsException
        at java.io.FileInputStream.readBytes(Native Method)
        at java.io.FileInputStream.read(FileInputStream.java:199)
        at java.io.DataInputStream.read(DataInputStream.java:132)
        at org.biojava.bio.program.scf.SCF$Parser.parsePrivate(SCF.java:391)
        at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:349)
        at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:202)
        at org.biojava.bio.program.scf.SCF.load(SCF.java:145)
        at org.biojava.bio.program.scf.SCF.load(SCF.java:140)
        at org.biojava.bio.program.scf.SCF.create(SCF.java:126)

1.5-beta2 version of SCF class.


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From bugzilla-daemon at portal.open-bio.org  Wed Jan  3 12:13:54 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 3 Jan 2007 12:13:54 -0500
Subject: [Biojava-dev] [Bug 2175] IndexOutOfBoundsException still occurring
	on SCF.create(File file)
In-Reply-To: <bug-2175-485@http.bugzilla.open-bio.org/>
Message-ID: <200701031713.l03HDsoN016548@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2175


holland at ebi.ac.uk changed:

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




------- Comment #2 from holland at ebi.ac.uk  2007-01-03 12:13 -------
1) please check that your SCF file is version 2 or version 3. More recent
versions are not yet supported.

2) the exception occurs whilst parsing a PRIVATE block in your SCF file. The
block is supposed to specify its size in the header and its offset from the
start, then the parser uses this size to read exactly the right amount of data
from the right location. In your case it sounds like the header contains an
incorrect (too large) size or an incorrect (too late) offset, and so the parser
is attempting to read more data than is actually present at the given offset.
This would be a bug in the SCF file not the parser.

Please could you check the above and get back to me - the file itself would be
useful too.


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From mark.schreiber at novartis.com  Wed Jan  3 22:14:36 2007
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Thu, 4 Jan 2007 11:14:36 +0800
Subject: [Biojava-dev] nio for io?
Message-ID: <OF148E290B.B091F08E-ON48257259.001133E5-48257259.0011D10E@ah.novartis.com>

Hello -

I have been reading about the NIO api recently (very remiss of me to leave 
it this long). There seems to be potential for this to greatly speed up 
our parsers such as memory mapping etc, however ....

Our current Format objects want to see something like a BufferedReader. We 
would probably need to make an extension to the Format interface to use a 
FileChannel of some sort as input.

If I do something so naive as use the Channels utility to wrap a Channel 
into a BufferedReader I get no advantage (it's even a bit slower).

There has been some talk of Sun reprogramming normal java.io objects to 
use NIO internally, does anyone know if this has happened (if it has there 
is probably not much point in us looking into it much)?

Are there people more experienced with this API that can see some 
potential for it to improve parsing speed (probably the biggest 
bioinformatics bottleneck)? Comments greatly appreciated.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910


From heuermh at acm.org  Thu Jan  4 01:02:55 2007
From: heuermh at acm.org (Michael Heuer)
Date: Thu, 4 Jan 2007 01:02:55 -0500 (EST)
Subject: [Biojava-dev] nio for io?
In-Reply-To: <OF148E290B.B091F08E-ON48257259.001133E5-48257259.0011D10E@ah.novartis.com>
Message-ID: <Pine.GSO.4.44.0701040057380.7916-100000@shell3.shore.net>

Mark Schreiber wrote:

> There has been some talk of Sun reprogramming normal java.io objects to
> use NIO internally, does anyone know if this has happened (if it has there
> is probably not much point in us looking into it much)?

I seem to remember the jdk release notes around 1.5 saying this was the
case.

Very unscientifically,

$ grep nio jdk1.6.0/src/java/io/*.java
ByteArrayOutputStream.java:     * default character set. The {@linkplain
java.nio.charset.CharsetDecoder}
ByteArrayOutputStream.java:     * the specified {@link
java.nio.charset.Charset charsetName}. The length of
ByteArrayOutputStream.java:     * java.nio.charset.CharsetDecoder} class
should be used when more control
ByteArrayOutputStream.java:     *                   {@linkplain
java.nio.charset.Charset </code>charset<code>}
Console.java:import java.nio.charset.Charset;
Console.java:import sun.nio.cs.StreamDecoder;
Console.java:import sun.nio.cs.StreamEncoder;
Console.java:    * {@link java.io.Reader#read(java.nio.CharBuffer)
read(java.nio.CharBuffer)}
File.java:     * {@link java.nio.channels.FileLock FileLock}
File.java:     * {@link java.nio.channels.FileLock FileLock}
FileInputStream.java:import java.nio.channels.FileChannel;
FileInputStream.java:import sun.nio.ch.FileChannelImpl;
FileInputStream.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
FileInputStream.java:     * <p> The initial {@link
java.nio.channels.FileChannel#position()
FileOutputStream.java:import java.nio.channels.FileChannel;
FileOutputStream.java:import sun.nio.ch.FileChannelImpl;
FileOutputStream.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
FileOutputStream.java:     * <p> The initial {@link
java.nio.channels.FileChannel#position()
InputStreamReader.java:import java.nio.charset.Charset;
InputStreamReader.java:import java.nio.charset.CharsetDecoder;
InputStreamReader.java:import sun.nio.cs.StreamDecoder;
InputStreamReader.java: * java.nio.charset.Charset <code>charset</code>}.
The charset that it uses
InputStreamReader.java: * @see java.nio.charset.Charset
InputStreamReader.java:     *         {@link java.nio.charset.Charset
</code>charset<code>}
InputStreamReader.java:     * @see java.nio.charset.Charset
OutputStreamWriter.java:import java.nio.charset.Charset;
OutputStreamWriter.java:import java.nio.charset.CharsetEncoder;
OutputStreamWriter.java:import sun.nio.cs.StreamEncoder;
OutputStreamWriter.java: * java.nio.charset.Charset <code>charset</code>}.
The charset that it uses
OutputStreamWriter.java: * The {@linkplain
java.nio.charset.CharsetEncoder} class should be used when more
OutputStreamWriter.java: * @see java.nio.charset.Charset
OutputStreamWriter.java:     *         {@link java.nio.charset.Charset
</code>charset<code>}
OutputStreamWriter.java:     * @see java.nio.charset.Charset
PrintStream.java:     * {@linkplain
java.nio.charset.Charset#defaultCharset() default charset}
PrintStream.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintStream.java:     * java.nio.charset.Charset#defaultCharset() default
charset} for this
PrintStream.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintWriter.java:     * java.nio.charset.Charset#defaultCharset() default
charset} for this
PrintWriter.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintWriter.java:     * java.nio.charset.Charset#defaultCharset() default
charset} for this
PrintWriter.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
RandomAccessFile.java:import java.nio.channels.FileChannel;
RandomAccessFile.java:import sun.nio.ch.FileChannelImpl;
RandomAccessFile.java:     * java.nio.channels.FileChannel#force(boolean)
force(boolean)} method of
RandomAccessFile.java:     * the {@link java.nio.channels.FileChannel}
class, passing arguments of
RandomAccessFile.java:     * @see
java.nio.channels.FileChannel#force(boolean)
RandomAccessFile.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
RandomAccessFile.java:     * <p> The {@link
java.nio.channels.FileChannel#position()
Reader.java:    public int read(java.nio.CharBuffer target) throws
IOException {


$ grep nio jdk1.5.0_08/src/java/io/*.java
File.java:     * {@link java.nio.channels.FileLock FileLock}
File.java:     * {@link java.nio.channels.FileLock FileLock}
FileInputStream.java:import java.nio.channels.FileChannel;
FileInputStream.java:import sun.nio.ch.FileChannelImpl;
FileInputStream.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
FileInputStream.java:     * <p> The initial {@link
java.nio.channels.FileChannel#position()
FileOutputStream.java:import java.nio.channels.FileChannel;
FileOutputStream.java:import sun.nio.ch.FileChannelImpl;
FileOutputStream.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
FileOutputStream.java:     * <p> The initial {@link
java.nio.channels.FileChannel#position()
InputStreamReader.java:import java.nio.charset.Charset;
InputStreamReader.java:import java.nio.charset.CharsetDecoder;
InputStreamReader.java:import sun.nio.cs.StreamDecoder;
InputStreamReader.java: * java.nio.charset.Charset <code>charset</code>}.
The charset that it uses
InputStreamReader.java: * @see java.nio.charset.Charset
InputStreamReader.java:     *         {@link java.nio.charset.Charset
</code>charset<code>}
InputStreamReader.java:     * @see java.nio.charset.Charset
OutputStreamWriter.java:import java.nio.charset.Charset;
OutputStreamWriter.java:import java.nio.charset.CharsetEncoder;
OutputStreamWriter.java:import sun.nio.cs.StreamEncoder;
OutputStreamWriter.java: * java.nio.charset.Charset <code>charset</code>}.
The charset that it uses
OutputStreamWriter.java: * @see java.nio.charset.Charset
OutputStreamWriter.java:     *         {@link java.nio.charset.Charset
</code>charset<code>}
OutputStreamWriter.java:     * @see java.nio.charset.Charset
PrintStream.java:     * {@linkplain
java.nio.charset.Charset#defaultCharset default charset}
PrintStream.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintStream.java:     * java.nio.charset.Charset#defaultCharset default
charset} for this
PrintStream.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintWriter.java:     * java.nio.charset.Charset#defaultCharset default
charset} for this
PrintWriter.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintWriter.java:     * java.nio.charset.Charset#defaultCharset default
charset} for this
PrintWriter.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
RandomAccessFile.java:import java.nio.channels.FileChannel;
RandomAccessFile.java:import sun.nio.ch.FileChannelImpl;
RandomAccessFile.java:     * java.nio.channels.FileChannel#force(boolean)
force(boolean)} method of
RandomAccessFile.java:     * the {@link java.nio.channels.FileChannel}
class, passing arguments of
RandomAccessFile.java:     * @see
java.nio.channels.FileChannel#force(boolean)
RandomAccessFile.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
RandomAccessFile.java:     * <p> The {@link
java.nio.channels.FileChannel#position()
Reader.java:    public int read(java.nio.CharBuffer target) throws
IOException {

:)

   michael


From mark.schreiber at novartis.com  Thu Jan  4 01:26:51 2007
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Thu, 4 Jan 2007 14:26:51 +0800
Subject: [Biojava-dev] nio for io?
Message-ID: <OF19604BED.EC856085-ON48257259.00231D44-48257259.00236B25@ah.novartis.com>

OK , probably no gains to be made here then. Another good reason for 
people to upgrade to 1.5 or 1.6 if they have not already done so.

It may also explain why things slowed down when I used the converter in 
Channels. I was wrapping a Channel into something that already used one.

- Mark





Michael Heuer <heuermh at acm.org>
Sent by: biojava-dev-bounces at lists.open-bio.org
01/04/2007 02:02 PM

 
        To:     mark.schreiber at novartis.com
        cc:     biojava-dev at biojava.org
        Subject:        Re: [Biojava-dev] nio for io?


Mark Schreiber wrote:

> There has been some talk of Sun reprogramming normal java.io objects to
> use NIO internally, does anyone know if this has happened (if it has 
there
> is probably not much point in us looking into it much)?

I seem to remember the jdk release notes around 1.5 saying this was the
case.

Very unscientifically,

$ grep nio jdk1.6.0/src/java/io/*.java
ByteArrayOutputStream.java:     * default character set. The {@linkplain
java.nio.charset.CharsetDecoder}
ByteArrayOutputStream.java:     * the specified {@link
java.nio.charset.Charset charsetName}. The length of
ByteArrayOutputStream.java:     * java.nio.charset.CharsetDecoder} class
should be used when more control
ByteArrayOutputStream.java:     *                   {@linkplain
java.nio.charset.Charset </code>charset<code>}
Console.java:import java.nio.charset.Charset;
Console.java:import sun.nio.cs.StreamDecoder;
Console.java:import sun.nio.cs.StreamEncoder;
Console.java:    * {@link java.io.Reader#read(java.nio.CharBuffer)
read(java.nio.CharBuffer)}
File.java:     * {@link java.nio.channels.FileLock FileLock}
File.java:     * {@link java.nio.channels.FileLock FileLock}
FileInputStream.java:import java.nio.channels.FileChannel;
FileInputStream.java:import sun.nio.ch.FileChannelImpl;
FileInputStream.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
FileInputStream.java:     * <p> The initial {@link
java.nio.channels.FileChannel#position()
FileOutputStream.java:import java.nio.channels.FileChannel;
FileOutputStream.java:import sun.nio.ch.FileChannelImpl;
FileOutputStream.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
FileOutputStream.java:     * <p> The initial {@link
java.nio.channels.FileChannel#position()
InputStreamReader.java:import java.nio.charset.Charset;
InputStreamReader.java:import java.nio.charset.CharsetDecoder;
InputStreamReader.java:import sun.nio.cs.StreamDecoder;
InputStreamReader.java: * java.nio.charset.Charset <code>charset</code>}.
The charset that it uses
InputStreamReader.java: * @see java.nio.charset.Charset
InputStreamReader.java:     *         {@link java.nio.charset.Charset
</code>charset<code>}
InputStreamReader.java:     * @see java.nio.charset.Charset
OutputStreamWriter.java:import java.nio.charset.Charset;
OutputStreamWriter.java:import java.nio.charset.CharsetEncoder;
OutputStreamWriter.java:import sun.nio.cs.StreamEncoder;
OutputStreamWriter.java: * java.nio.charset.Charset <code>charset</code>}.
The charset that it uses
OutputStreamWriter.java: * The {@linkplain
java.nio.charset.CharsetEncoder} class should be used when more
OutputStreamWriter.java: * @see java.nio.charset.Charset
OutputStreamWriter.java:     *         {@link java.nio.charset.Charset
</code>charset<code>}
OutputStreamWriter.java:     * @see java.nio.charset.Charset
PrintStream.java:     * {@linkplain
java.nio.charset.Charset#defaultCharset() default charset}
PrintStream.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintStream.java:     * java.nio.charset.Charset#defaultCharset() default
charset} for this
PrintStream.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintWriter.java:     * java.nio.charset.Charset#defaultCharset() default
charset} for this
PrintWriter.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintWriter.java:     * java.nio.charset.Charset#defaultCharset() default
charset} for this
PrintWriter.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
RandomAccessFile.java:import java.nio.channels.FileChannel;
RandomAccessFile.java:import sun.nio.ch.FileChannelImpl;
RandomAccessFile.java:     * java.nio.channels.FileChannel#force(boolean)
force(boolean)} method of
RandomAccessFile.java:     * the {@link java.nio.channels.FileChannel}
class, passing arguments of
RandomAccessFile.java:     * @see
java.nio.channels.FileChannel#force(boolean)
RandomAccessFile.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
RandomAccessFile.java:     * <p> The {@link
java.nio.channels.FileChannel#position()
Reader.java:    public int read(java.nio.CharBuffer target) throws
IOException {


$ grep nio jdk1.5.0_08/src/java/io/*.java
File.java:     * {@link java.nio.channels.FileLock FileLock}
File.java:     * {@link java.nio.channels.FileLock FileLock}
FileInputStream.java:import java.nio.channels.FileChannel;
FileInputStream.java:import sun.nio.ch.FileChannelImpl;
FileInputStream.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
FileInputStream.java:     * <p> The initial {@link
java.nio.channels.FileChannel#position()
FileOutputStream.java:import java.nio.channels.FileChannel;
FileOutputStream.java:import sun.nio.ch.FileChannelImpl;
FileOutputStream.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
FileOutputStream.java:     * <p> The initial {@link
java.nio.channels.FileChannel#position()
InputStreamReader.java:import java.nio.charset.Charset;
InputStreamReader.java:import java.nio.charset.CharsetDecoder;
InputStreamReader.java:import sun.nio.cs.StreamDecoder;
InputStreamReader.java: * java.nio.charset.Charset <code>charset</code>}.
The charset that it uses
InputStreamReader.java: * @see java.nio.charset.Charset
InputStreamReader.java:     *         {@link java.nio.charset.Charset
</code>charset<code>}
InputStreamReader.java:     * @see java.nio.charset.Charset
OutputStreamWriter.java:import java.nio.charset.Charset;
OutputStreamWriter.java:import java.nio.charset.CharsetEncoder;
OutputStreamWriter.java:import sun.nio.cs.StreamEncoder;
OutputStreamWriter.java: * java.nio.charset.Charset <code>charset</code>}.
The charset that it uses
OutputStreamWriter.java: * @see java.nio.charset.Charset
OutputStreamWriter.java:     *         {@link java.nio.charset.Charset
</code>charset<code>}
OutputStreamWriter.java:     * @see java.nio.charset.Charset
PrintStream.java:     * {@linkplain
java.nio.charset.Charset#defaultCharset default charset}
PrintStream.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintStream.java:     * java.nio.charset.Charset#defaultCharset default
charset} for this
PrintStream.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintWriter.java:     * java.nio.charset.Charset#defaultCharset default
charset} for this
PrintWriter.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintWriter.java:     * java.nio.charset.Charset#defaultCharset default
charset} for this
PrintWriter.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
RandomAccessFile.java:import java.nio.channels.FileChannel;
RandomAccessFile.java:import sun.nio.ch.FileChannelImpl;
RandomAccessFile.java:     * java.nio.channels.FileChannel#force(boolean)
force(boolean)} method of
RandomAccessFile.java:     * the {@link java.nio.channels.FileChannel}
class, passing arguments of
RandomAccessFile.java:     * @see
java.nio.channels.FileChannel#force(boolean)
RandomAccessFile.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
RandomAccessFile.java:     * <p> The {@link
java.nio.channels.FileChannel#position()
Reader.java:    public int read(java.nio.CharBuffer target) throws
IOException {

:)

   michael

_______________________________________________
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From bugzilla-daemon at portal.open-bio.org  Thu Jan  4 11:54:06 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 4 Jan 2007 11:54:06 -0500
Subject: [Biojava-dev] [Bug 2175] IndexOutOfBoundsException still occurring
	on SCF.create(File file)
In-Reply-To: <bug-2175-485@http.bugzilla.open-bio.org/>
Message-ID: <200701041654.l04Gs6NG014233@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2175


holland at ebi.ac.uk changed:

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




------- Comment #3 from holland at ebi.ac.uk  2007-01-04 11:54 -------
I've added a workaround to this in the head of CVS, but not in the beta
branches etc.

Basically I was right - the file given as an example has incorrect values in
its header data declaring that the private block is much bigger (835) than it
actually is (698). 

The workaround causes the parser to notice this and not attempt to read the
excess data. As the private block is not used anywhere inside the parser class
and is not visible to outside users, this should not affect anyone's code.


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From bugzilla-daemon at portal.open-bio.org  Fri Jan  5 05:16:02 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 5 Jan 2007 05:16:02 -0500
Subject: [Biojava-dev] [Bug 2177] New: Unclosed streams in
	org.biojava.bio.program.scf.SCF
Message-ID: <bug-2177-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2177

           Summary: Unclosed streams in org.biojava.bio.program.scf.SCF
           Product: BioJava
           Version: 1.4
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: major
          Priority: P2
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: keiranmraine at gmail.com


Hi,

There are problems in the following methods where the input streams have not
been closed.  This can cause a 'too many open files' os error when working
rapidly over large data sets.

org.biojava.bio.program.scf.SCF.load(File f)
- FileInputStream fin;

org.biojava.bio.program.scf.SCF.ParserFactory.parse(InputStream in, SCF out,
long initOffset)
 - DataInputStream din


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From bugzilla-daemon at portal.open-bio.org  Fri Jan  5 05:42:45 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 5 Jan 2007 05:42:45 -0500
Subject: [Biojava-dev] [Bug 2177] Unclosed streams in
	org.biojava.bio.program.scf.SCF
In-Reply-To: <bug-2177-485@http.bugzilla.open-bio.org/>
Message-ID: <200701051042.l05Agj4l030583@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2177





------- Comment #1 from andyyatz at gmail.com  2007-01-05 05:42 -------
(In reply to comment #0)
> Hi,
> 
> There are problems in the following methods where the input streams have not
> been closed.  This can cause a 'too many open files' os error when working
> rapidly over large data sets.
> 
> org.biojava.bio.program.scf.SCF.load(File f)
> - FileInputStream fin;
> 
> org.biojava.bio.program.scf.SCF.ParserFactory.parse(InputStream in, SCF out,
> long initOffset)
>  - DataInputStream din
> 

After a quick look at the source:

1). Yes SCF.load(File f) needs to be changed to:

protected void load(File f) throws IOException,
  UnsupportedChromatogramFormatException {
  FileInputStream fin = new FileInputStream(f);
  try {
    load(fin, 0);
  }
  finally {
    fin.close();
  }
}

Since this method opens the InputStream to the SCF file it has to be
responsible for closing the stream.

2). I don't think that parse(InputStream in, SCF out, long initOffset) should
be closing streams since it does not create them. It should be creating
method's responsibility to close these streams.


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From bugzilla-daemon at portal.open-bio.org  Fri Jan  5 05:55:32 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 5 Jan 2007 05:55:32 -0500
Subject: [Biojava-dev] [Bug 2177] Unclosed streams in
	org.biojava.bio.program.scf.SCF
In-Reply-To: <bug-2177-485@http.bugzilla.open-bio.org/>
Message-ID: <200701051055.l05AtWi4031158@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2177





------- Comment #2 from andyyatz at gmail.com  2007-01-05 05:55 -------
Created an attachment (id=535)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=535&action=view)
Patch for SCF class

First patch file I've created so sorry if it is wrong but I've tested the
patching process on my machine and it seems to work. Can someone please do a
quick compile with patch for me please?


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From bugzilla-daemon at portal.open-bio.org  Fri Jan  5 06:07:01 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 5 Jan 2007 06:07:01 -0500
Subject: [Biojava-dev] [Bug 2177] Unclosed streams in
	org.biojava.bio.program.scf.SCF
In-Reply-To: <bug-2177-485@http.bugzilla.open-bio.org/>
Message-ID: <200701051107.l05B71LE031749@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2177





------- Comment #3 from holland at ebi.ac.uk  2007-01-05 06:07 -------
I've tested and applied Andy's patch in CVS head. All seems to work nicely now.


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From bugzilla-daemon at portal.open-bio.org  Fri Jan  5 06:07:21 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 5 Jan 2007 06:07:21 -0500
Subject: [Biojava-dev] [Bug 2177] Unclosed streams in
	org.biojava.bio.program.scf.SCF
In-Reply-To: <bug-2177-485@http.bugzilla.open-bio.org/>
Message-ID: <200701051107.l05B7L8f031793@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2177


holland at ebi.ac.uk changed:

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




------- Comment #4 from holland at ebi.ac.uk  2007-01-05 06:07 -------
I've tested and applied Andy's patch in CVS head. All seems to work nicely now.


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From bugzilla-daemon at portal.open-bio.org  Fri Jan  5 06:10:07 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 5 Jan 2007 06:10:07 -0500
Subject: [Biojava-dev] [Bug 2177] Unclosed streams in
	org.biojava.bio.program.scf.SCF
In-Reply-To: <bug-2177-485@http.bugzilla.open-bio.org/>
Message-ID: <200701051110.l05BA7tM031932@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2177


keiranmraine at gmail.com changed:

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




------- Comment #5 from keiranmraine at gmail.com  2007-01-05 06:10 -------
I don't mean the input stream in the second method.  It's the DataInputStream
that should be closed here, see below.

public static void parse(InputStream in, SCF out, long initOffset)
        throws IOException, UnsupportedChromatogramFormatException {
  DataInputStream din;
  try {
    din = new DataInputStream(in);
    SCF.Parser parser = createParser(din, out, initOffset);
    parser.parse();
  }
  finally {
    din.close();
  }
}


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From bugzilla-daemon at portal.open-bio.org  Fri Jan  5 06:21:14 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 5 Jan 2007 06:21:14 -0500
Subject: [Biojava-dev] [Bug 2177] Unclosed streams in
	org.biojava.bio.program.scf.SCF
In-Reply-To: <bug-2177-485@http.bugzilla.open-bio.org/>
Message-ID: <200701051121.l05BLEXp032535@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2177


holland at ebi.ac.uk changed:

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




------- Comment #6 from holland at ebi.ac.uk  2007-01-05 06:21 -------
Publicly visible methods that accept InputStreams should never ever close them
- that is the responsibility of the caller. If the DataInputStream wrapping the
InputStream were closed, it would also close the InputStream, thus breaking
this contract. The DataInputStream will be implicitly closed when the caller
closes the original InputStream after calling the method in question.


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From bugzilla-daemon at portal.open-bio.org  Fri Jan  5 06:27:30 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 5 Jan 2007 06:27:30 -0500
Subject: [Biojava-dev] [Bug 2177] Unclosed streams in
	org.biojava.bio.program.scf.SCF
In-Reply-To: <bug-2177-485@http.bugzilla.open-bio.org/>
Message-ID: <200701051127.l05BRUUa000422@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2177





------- Comment #7 from keiranmraine at gmail.com  2007-01-05 06:27 -------
(In reply to comment #6)
> Publicly visible methods that accept InputStreams should never ever close them
> - that is the responsibility of the caller. If the DataInputStream wrapping the
> InputStream were closed, it would also close the InputStream, thus breaking
> this contract. The DataInputStream will be implicitly closed when the caller
> closes the original InputStream after calling the method in question.
> 

Ahhh, sorry sbout that, I did not realise that closing the DataInputStream
would close the InputStream.

Thanks


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From bugzilla-daemon at portal.open-bio.org  Tue Jan 16 12:35:53 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 16 Jan 2007 12:35:53 -0500
Subject: [Biojava-dev] [Bug 2186] New: ABIFparser never releases file
	resouce when generated with a File
Message-ID: <bug-2186-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2186

           Summary: ABIFparser never releases file resouce when generated
                    with a File
           Product: BioJava
           Version: 1.4
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: keiranmraine at gmail.com


Hi all,

I've detected a resource problem in the use of the following object constructor

org.biojava.bio.program.abi.ABIFParser(File f)

If you generate the parser in this manner the generated RandomAccessFile is
never closed and causes a resource leak.  The way the code is written I cannot
see an obvious place to close this, but there appears to be a simple fix in
that you can use the alternative method:

org.biojava.bio.program.abi.ABIFParser(InputStream in)

and control the closing outside of Biojava.

As I say I'm not sure at which point it's safe to close the stream in
ABIFParser but the File method could be removed??

Keiran


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 17 04:45:10 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 17 Jan 2007 04:45:10 -0500
Subject: [Biojava-dev] [Bug 2186] ABIFparser never releases file resouce
	when generated with a File
In-Reply-To: <bug-2186-485@http.bugzilla.open-bio.org/>
Message-ID: <200701170945.l0H9jAcx003234@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2186





------- Comment #1 from andyyatz at gmail.com  2007-01-17 04:45 -------
(In reply to comment #0)
> Hi all,
> 
> I've detected a resource problem in the use of the following object constructor
> 
> org.biojava.bio.program.abi.ABIFParser(File f)
> 
> If you generate the parser in this manner the generated RandomAccessFile is
> never closed and causes a resource leak.  The way the code is written I cannot
> see an obvious place to close this, but there appears to be a simple fix in
> that you can use the alternative method:
> 
> org.biojava.bio.program.abi.ABIFParser(InputStream in)
> 
> and control the closing outside of Biojava.
> 
> As I say I'm not sure at which point it's safe to close the stream in
> ABIFParser but the File method could be removed??
> 
> Keiran
> 

It would seem that way without a close method introduced into the parser which
then causes more problems. I would prefer a deprecation of the constructor to
warn future users that this is not the preferred way of creating an ABIFParser. 

Maybe an extension to this class should be a static builder method which takes
in a file, creates the required stream, passes out the finished object and
makes sure to clean up after itself. I don't know it this is possible as I've
only every gone into the guts of the ABI parser once.


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 17 05:41:45 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 17 Jan 2007 05:41:45 -0500
Subject: [Biojava-dev] [Bug 2186] ABIFparser never releases file resouce
	when generated with a File
In-Reply-To: <bug-2186-485@http.bugzilla.open-bio.org/>
Message-ID: <200701171041.l0HAfjR9005812@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2186


holland at ebi.ac.uk changed:

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




------- Comment #2 from holland at ebi.ac.uk  2007-01-17 05:41 -------
I found a way of changing it but it involved adding a method to the
ABIFParser.DataAccess interface. This does not affect anything internally to
BioJava but may affect user code - but I very much doubt anyone is using it.
Changes have been committed to the HEAD of biojava-live.


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 17 10:47:36 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 17 Jan 2007 10:47:36 -0500
Subject: [Biojava-dev] [Bug 2187] New: Stack trace printed:
	org.biojava.bio.program.scf.SCF$V3Parser.parseBases
Message-ID: <bug-2187-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2187

           Summary: Stack trace printed:
                    org.biojava.bio.program.scf.SCF$V3Parser.parseBases
           Product: BioJava
           Version: 1.4
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: keiranmraine at gmail.com


Hi,

Just a nicety for anyone using the class in programs for use by
non-programmers.

When catching the IllegalSymbolException the stack trace is printed in
org.biojava.bio.program.scf.SCF$V3Parser.parseBases.

I suggest that the UnsupportedChromatogramFormatException be extended to take
the Throwable and the 'ise.printStackTrace(System.err);' removed.

e.g.

catch (IllegalSymbolException ise) {
  ise.printStackTrace(System.err);
  throw new UnsupportedChromatogramFormatException("Base call decoding
failure");
}

BECOMES

catch (IllegalSymbolException ise) {
  throw new UnsupportedChromatogramFormatException("Base call decoding
failure", ise);
}


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 17 10:47:46 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 17 Jan 2007 10:47:46 -0500
Subject: [Biojava-dev] [Bug 2188] New: Stack trace printed:
	org.biojava.bio.program.scf.SCF$V3Parser.parseBases
Message-ID: <bug-2188-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2188

           Summary: Stack trace printed:
                    org.biojava.bio.program.scf.SCF$V3Parser.parseBases
           Product: BioJava
           Version: 1.4
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: keiranmraine at gmail.com


Hi,

Just a nicety for anyone using the class in programs for use by
non-programmers.

When catching the IllegalSymbolException the stack trace is printed in
org.biojava.bio.program.scf.SCF$V3Parser.parseBases.

I suggest that the UnsupportedChromatogramFormatException be extended to take
the Throwable and the 'ise.printStackTrace(System.err);' removed.

e.g.

catch (IllegalSymbolException ise) {
  ise.printStackTrace(System.err);
  throw new UnsupportedChromatogramFormatException("Base call decoding
failure");
}

BECOMES

catch (IllegalSymbolException ise) {
  throw new UnsupportedChromatogramFormatException("Base call decoding
failure", ise);
}


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 17 11:00:28 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 17 Jan 2007 11:00:28 -0500
Subject: [Biojava-dev] [Bug 2188] Stack trace printed:
	org.biojava.bio.program.scf.SCF$V3Parser.parseBases
In-Reply-To: <bug-2188-485@http.bugzilla.open-bio.org/>
Message-ID: <200701171600.l0HG0S0X030332@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2188


holland at ebi.ac.uk changed:

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




------- Comment #1 from holland at ebi.ac.uk  2007-01-17 11:00 -------


*** This bug has been marked as a duplicate of 2187 ***


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 17 11:00:32 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 17 Jan 2007 11:00:32 -0500
Subject: [Biojava-dev] [Bug 2187] Stack trace printed:
	org.biojava.bio.program.scf.SCF$V3Parser.parseBases
In-Reply-To: <bug-2187-485@http.bugzilla.open-bio.org/>
Message-ID: <200701171600.l0HG0WRv030352@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2187





------- Comment #1 from holland at ebi.ac.uk  2007-01-17 11:00 -------
*** Bug 2188 has been marked as a duplicate of this bug. ***


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 17 11:03:22 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 17 Jan 2007 11:03:22 -0500
Subject: [Biojava-dev] [Bug 2187] Stack trace printed:
	org.biojava.bio.program.scf.SCF$V3Parser.parseBases
In-Reply-To: <bug-2187-485@http.bugzilla.open-bio.org/>
Message-ID: <200701171603.l0HG3MZU030882@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2187


holland at ebi.ac.uk changed:

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




------- Comment #2 from holland at ebi.ac.uk  2007-01-17 11:03 -------
I've made the change as suggested. Committed to CVS biojava-live HEAD.


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From holland at ebi.ac.uk  Fri Jan 19 10:54:45 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Fri, 19 Jan 2007 15:54:45 -0000
Subject: [Biojava-dev] SimpleGFFRecord
In-Reply-To: <200612201658.02312.tamir@imp.univie.ac.at>
References: <200612201658.02312.tamir@imp.univie.ac.at>
Message-ID: <458963F3.9020706@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Thanks for pointing this out. I have fixed it on the HEAD branch of CVS.

cheers,
Richard

Ido M. Tamir wrote:
> 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);
>   }
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
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From ayates at ebi.ac.uk  Fri Jan 19 11:18:05 2007
From: ayates at ebi.ac.uk (Andy Yates)
Date: Fri, 19 Jan 2007 16:18:05 -0000
Subject: [Biojava-dev] how to run unittest in eclipse
In-Reply-To: <BAY7-F23C6E75109962FA246420CA5BA0@phx.gbl>
References: <BAY7-F23C6E75109962FA246420CA5BA0@phx.gbl>
Message-ID: <459A68DE.4020506@ebi.ac.uk>

Hi,

This sounds like a problem more with bad project setup where Eclipse has 
not been told where the resources directory is located.

In eclipse right click on the project and go to:

Build Path -> Configure Build Path...

Click on the source tab and then click on the button Add Folder. Select 
the resources directory from the root of the BioJava project and then 
click ok.

If everything has gone okay when you now run the test the Eclipse JUnit 
runner should pick up on the resources classpath and you should have a 
bit more luck with them.

Andy Yates

Huang Zhibin wrote:
> Dear all,
>  First all,thanks for the contribution of BioJava.
>  I downloaded the BioJava and compile apps, demos, tests and runtests 
> using ant. It is ok. But when importing this project into eclipse, I do 
> not know hot to runtests. For example, when clicking file of 
> /tests/org.biojava.bio.alignment/FlexibleAlignmentTest.java, choose Run 
> As | JUnit Test, it fails. Info in Console will be listed below.
>  I know maybe it failed in the step of initialization, but I do now know 
> how to solve it.
>  Can someone who run junittest in JAVA IDE share the experience or give 
> me some suggestions? I will appreciate it.
> Best regards,
> Zhibin
> 
> ------------------------------
> Info printed in Console:
> 
> org.biojava.bio.BioError: Unable to initialize DNATools
>     at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:117)
>     at 
> org.biojava.bio.alignment.FlexibleAlignmentTest.parse(FlexibleAlignmentTest.java:74) 
> 
> 
>     at 
> org.biojava.bio.alignment.FlexibleAlignmentTest.<clinit>(FlexibleAlignmentTest.java:46) 
> 
> 
>     at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native 
> Method)
>     at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown 
> Source)
>     at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown 
> Source)
>     at java.lang.reflect.Constructor.newInstance(Unknown Source)
>     at junit.framework.TestSuite.createTest(TestSuite.java:135)
>     at junit.framework.TestSuite.addTestMethod(TestSuite.java:114)
>     at junit.framework.TestSuite.<init>(TestSuite.java:75)
>     at 
> org.eclipse.jdt.internal.junit.runner.junit3.JUnit3TestLoader.getTest(JUnit3TestLoader.java:102) 
> 
> 
>     at 
> org.eclipse.jdt.internal.junit.runner.junit3.JUnit3TestLoader.loadTests(JUnit3TestLoader.java:59) 
> 
> 
>     at 
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:445) 
> 
> 
>     at 
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:673) 
> 
> 
>     at 
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:386) 
> 
> 
>     at 
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:196) 
> 
> 
> Caused by: org.biojava.bio.BioError: Couldn't locate 
> AlphabetManager.xml.  This probably means that your biojava.jar file is 
> corrupt or incorrectly built.
>     at 
> org.biojava.bio.symbol.AlphabetManager.<clinit>(AlphabetManager.java:148)
>     at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:80)
>     ... 15 more
> java.lang.NoClassDefFoundError
>     at org.biojava.bio.seq.ProteinTools.<clinit>(ProteinTools.java:76)
>     at 
> org.biojava.bio.alignment.FlexibleAlignmentTest.parse(FlexibleAlignmentTest.java:76) 
> 
> 
> 
> _________________________________________________________________
> ??????????,??? MSN Messenger:  http://messenger.msn.com/cn 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev

From td2 at sanger.ac.uk  Wed Jan 31 04:53:21 2007
From: td2 at sanger.ac.uk (Thomas Down)
Date: Wed, 31 Jan 2007 09:53:21 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
Message-ID: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>

Hi,

A few weeks ago, this patch removed a couple of apparently-redundant  
lines from JDBCPooledDataSource:

               http://code.open-bio.org/cgi/viewcvs.cgi/biojava-live/ 
src/org/biojava/utils/JDBCPooledDataSource.java.diff? 
r1=1.2&r2=1.3&cvsroot=biojava

This change causes at least some DataSource objects created using  
this class to fail with a NullPointerException the first time a  
connection is actually requested.  Using biojava-ensembl to access an  
Ensembl MySQL database demonstrates this problem consistently.   
Reverting to revision 1.2 of JDBCPooledDataSource.java solves the  
problem.

It looks like the PoolableConnectionFactory constructor has a side  
effect of registering the factory with the specified ObjectPool.   
This side effect doesn't seem to be documented particularly clearly,  
but the example code towards the bottom of:

           http://jakarta.apache.org/commons/dbcp/apidocs/org/apache/ 
commons/dbcp/package-summary.html#package_description

seems to rely on this behavior.


Would it be possible to roll this source file back to revision 1.2?   
Or, alternatively, is there someone who can set me up with commit  
access on the new CVS server (I think I still have an account there,  
but my password doesn't work since the server move).

Thanks,

                Thomas.

From holland at ebi.ac.uk  Wed Jan 31 06:04:05 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 31 Jan 2007 11:04:05 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
Message-ID: <45C077A5.4070706@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi Thomas. I have made the change on Head as you have requested.

cheers,
Richard.

Thomas Down wrote:
> Hi,
> 
> A few weeks ago, this patch removed a couple of apparently-redundant  
> lines from JDBCPooledDataSource:
> 
>                http://code.open-bio.org/cgi/viewcvs.cgi/biojava-live/ 
> src/org/biojava/utils/JDBCPooledDataSource.java.diff? 
> r1=1.2&r2=1.3&cvsroot=biojava
> 
> This change causes at least some DataSource objects created using  
> this class to fail with a NullPointerException the first time a  
> connection is actually requested.  Using biojava-ensembl to access an  
> Ensembl MySQL database demonstrates this problem consistently.   
> Reverting to revision 1.2 of JDBCPooledDataSource.java solves the  
> problem.
> 
> It looks like the PoolableConnectionFactory constructor has a side  
> effect of registering the factory with the specified ObjectPool.   
> This side effect doesn't seem to be documented particularly clearly,  
> but the example code towards the bottom of:
> 
>            http://jakarta.apache.org/commons/dbcp/apidocs/org/apache/ 
> commons/dbcp/package-summary.html#package_description
> 
> seems to rely on this behavior.
> 
> 
> Would it be possible to roll this source file back to revision 1.2?   
> Or, alternatively, is there someone who can set me up with commit  
> access on the new CVS server (I think I still have an account there,  
> but my password doesn't work since the server move).
> 
> Thanks,
> 
>                 Thomas.
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
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From ayates at ebi.ac.uk  Wed Jan 31 06:06:03 2007
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 31 Jan 2007 11:06:03 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
Message-ID: <45C0781B.7030304@ebi.ac.uk>

Hi,

I would say that this class' method is trying to do too much. We have a 
method which is creating a BasicDataSource then not bothering to return 
it in favour of a custom one which implements a hashcode & equals 
method. Can you try your test case when it returns the BasicDataSource & 
not the custom one and see if that works please?

Thanks,

Andy Yates

Thomas Down wrote:
> Hi,
> 
> A few weeks ago, this patch removed a couple of apparently-redundant  
> lines from JDBCPooledDataSource:
> 
>                http://code.open-bio.org/cgi/viewcvs.cgi/biojava-live/ 
> src/org/biojava/utils/JDBCPooledDataSource.java.diff? 
> r1=1.2&r2=1.3&cvsroot=biojava
> 
> This change causes at least some DataSource objects created using  
> this class to fail with a NullPointerException the first time a  
> connection is actually requested.  Using biojava-ensembl to access an  
> Ensembl MySQL database demonstrates this problem consistently.   
> Reverting to revision 1.2 of JDBCPooledDataSource.java solves the  
> problem.
> 
> It looks like the PoolableConnectionFactory constructor has a side  
> effect of registering the factory with the specified ObjectPool.   
> This side effect doesn't seem to be documented particularly clearly,  
> but the example code towards the bottom of:
> 
>            http://jakarta.apache.org/commons/dbcp/apidocs/org/apache/ 
> commons/dbcp/package-summary.html#package_description
> 
> seems to rely on this behavior.
> 
> 
> Would it be possible to roll this source file back to revision 1.2?   
> Or, alternatively, is there someone who can set me up with commit  
> access on the new CVS server (I think I still have an account there,  
> but my password doesn't work since the server move).
> 
> Thanks,
> 
>                 Thomas.
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev

From td2 at sanger.ac.uk  Wed Jan 31 06:59:31 2007
From: td2 at sanger.ac.uk (Thomas Down)
Date: Wed, 31 Jan 2007 11:59:31 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <45C0781B.7030304@ebi.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
	<45C0781B.7030304@ebi.ac.uk>
Message-ID: <5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>


On 31 Jan 2007, at 11:06, Andy Yates wrote:

> Hi,
>
> I would say that this class' method is trying to do too much. We  
> have a
> method which is creating a BasicDataSource then not bothering to  
> return
> it in favour of a custom one which implements a hashcode & equals
> method. Can you try your test case when it returns the  
> BasicDataSource &
> not the custom one and see if that works please?

Patching the current revision to return a PoolingDataSource (I assume  
that's what you meant) rather than a MyPoolingDataSource works fine.   
However, patching revision 1.3 the same way does not work.  The  
problem I reported is definitely orthogonal to the question of  
exactly which type of PoolingDataSource gets returned.

I'm not sure what the original rationale was for returning the custom  
PoolingDataSource subclass -- but I can't really see how it's going  
to do any harm.

            Thomas.

From ayates at ebi.ac.uk  Wed Jan 31 07:06:17 2007
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 31 Jan 2007 12:06:17 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
	<45C0781B.7030304@ebi.ac.uk>
	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>
Message-ID: <45C08639.7080600@ebi.ac.uk>

Hi,

Sorry I was meaning if that if that method just becomes:

public static DataSource getDataSource(final String driver,
                                          final String url,
                                          final String user,
                                          final String pass)
     throws Exception {

     BasicDataSource ds = new BasicDataSource();
     ds.setUrl(url);
     ds.setDriverClassName(driver);
     ds.setUsername(user);
     ds.setPassword(pass);
     // Set BasicDataSource properties such as maxActive and maxIdle, as 
described in
     // 
http://jakarta.apache.org/commons/dbcp/api/org/apache/commons/dbcp/BasicDataSource.html
     ds.setMaxActive(10);
     ds.setMaxIdle(5);
     ds.setMaxWait(10000);

     return ds;
   }

Does that still work?

I think the original rationale was to ensure that any two datasources do 
actually point to the same resource. However this seems a bit too much 
defensive programming & I don't know why anyone would program themselves 
into a situation where this is required.

Andy

Thomas Down wrote:
> 
> On 31 Jan 2007, at 11:06, Andy Yates wrote:
> 
>> Hi,
>>
>> I would say that this class' method is trying to do too much. We have a
>> method which is creating a BasicDataSource then not bothering to return
>> it in favour of a custom one which implements a hashcode & equals
>> method. Can you try your test case when it returns the BasicDataSource &
>> not the custom one and see if that works please?
> 
> Patching the current revision to return a PoolingDataSource (I assume 
> that's what you meant) rather than a MyPoolingDataSource works fine.  
> However, patching revision 1.3 the same way does not work.  The problem 
> I reported is definitely orthogonal to the question of exactly which 
> type of PoolingDataSource gets returned.
> 
> I'm not sure what the original rationale was for returning the custom 
> PoolingDataSource subclass -- but I can't really see how it's going to 
> do any harm.
> 
>            Thomas.

From td2 at sanger.ac.uk  Wed Jan 31 07:21:10 2007
From: td2 at sanger.ac.uk (Thomas Down)
Date: Wed, 31 Jan 2007 12:21:10 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <45C08639.7080600@ebi.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
	<45C0781B.7030304@ebi.ac.uk>
	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>
	<45C08639.7080600@ebi.ac.uk>
Message-ID: <8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>


On 31 Jan 2007, at 12:06, Andy Yates wrote:

> Hi,
>
> Sorry I was meaning if that if that method just becomes:
>
> public static DataSource getDataSource(final String driver,
>                                          final String url,
>                                          final String user,
>                                          final String pass)
>     throws Exception {
>
>     BasicDataSource ds = new BasicDataSource();
>     ds.setUrl(url);
>     ds.setDriverClassName(driver);
>     ds.setUsername(user);
>     ds.setPassword(pass);
>     // Set BasicDataSource properties such as maxActive and  
> maxIdle, as described in
>     // http://jakarta.apache.org/commons/dbcp/api/org/apache/ 
> commons/dbcp/BasicDataSource.html
>     ds.setMaxActive(10);
>     ds.setMaxIdle(5);
>     ds.setMaxWait(10000);
>
>     return ds;
>   }
>
> Does that still work?

Hmmm, I was assuming that BasicDataSource didn't actually do any  
pooling itself, and that you needed another layer on top to manage a  
connection pool -- that seems to be how all previous revisions of  
JDBCConnectionPool worked, so I guess I wasn't alone in thinking  
this.  But yes, BasicDataSource does seem to do pooling itself  
(confirmed by reading the source), so maybe your simpler version is a  
better idea.  It certainly works okay for me.

            Thomas.

From ayates at ebi.ac.uk  Wed Jan 31 07:28:42 2007
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 31 Jan 2007 12:28:42 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
	<45C0781B.7030304@ebi.ac.uk>
	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>
	<45C08639.7080600@ebi.ac.uk>
	<8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>
Message-ID: <45C08B7A.3060102@ebi.ac.uk>



Thomas Down wrote:
> 
> On 31 Jan 2007, at 12:06, Andy Yates wrote:
> 
>> Hi,
>>
>> Sorry I was meaning if that if that method just becomes:
>>
>> public static DataSource getDataSource(final String driver,
>>                                          final String url,
>>                                          final String user,
>>                                          final String pass)
>>     throws Exception {
>>
>>     BasicDataSource ds = new BasicDataSource();
>>     ds.setUrl(url);
>>     ds.setDriverClassName(driver);
>>     ds.setUsername(user);
>>     ds.setPassword(pass);
>>     // Set BasicDataSource properties such as maxActive and maxIdle, 
>> as described in
>>     // 
>> http://jakarta.apache.org/commons/dbcp/api/org/apache/commons/dbcp/BasicDataSource.html 
>>
>>     ds.setMaxActive(10);
>>     ds.setMaxIdle(5);
>>     ds.setMaxWait(10000);
>>
>>     return ds;
>>   }
>>
>> Does that still work?
> 
> Hmmm, I was assuming that BasicDataSource didn't actually do any pooling 
> itself, and that you needed another layer on top to manage a connection 
> pool -- that seems to be how all previous revisions of 
> JDBCConnectionPool worked, so I guess I wasn't alone in thinking this.  
> But yes, BasicDataSource does seem to do pooling itself (confirmed by 
> reading the source), so maybe your simpler version is a better idea.  It 
> certainly works okay for me.
> 
>            Thomas.

That's what I thought should have happened :). Can I suggest that this 
revised version goes into CVS? Anyone got any objections?

Andy

From holland at ebi.ac.uk  Wed Jan 31 07:40:46 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 31 Jan 2007 12:40:46 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <45C08B7A.3060102@ebi.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>	<45C0781B.7030304@ebi.ac.uk>	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>	<45C08639.7080600@ebi.ac.uk>	<8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>
	<45C08B7A.3060102@ebi.ac.uk>
Message-ID: <45C08E4E.2050308@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Andy could you make the change to your local copy of the source file and
email the file to me, that way I can make sure I don't get it wrong when
I commit it.

Richard.

PS. You should probably have your own CVS account - email the OBF
helpdesk and ask for one, saying I told you to. :)


Andy Yates wrote:
> 
> Thomas Down wrote:
>> On 31 Jan 2007, at 12:06, Andy Yates wrote:
>>
>>> Hi,
>>>
>>> Sorry I was meaning if that if that method just becomes:
>>>
>>> public static DataSource getDataSource(final String driver,
>>>                                          final String url,
>>>                                          final String user,
>>>                                          final String pass)
>>>     throws Exception {
>>>
>>>     BasicDataSource ds = new BasicDataSource();
>>>     ds.setUrl(url);
>>>     ds.setDriverClassName(driver);
>>>     ds.setUsername(user);
>>>     ds.setPassword(pass);
>>>     // Set BasicDataSource properties such as maxActive and maxIdle, 
>>> as described in
>>>     // 
>>> http://jakarta.apache.org/commons/dbcp/api/org/apache/commons/dbcp/BasicDataSource.html 
>>>
>>>     ds.setMaxActive(10);
>>>     ds.setMaxIdle(5);
>>>     ds.setMaxWait(10000);
>>>
>>>     return ds;
>>>   }
>>>
>>> Does that still work?
>> Hmmm, I was assuming that BasicDataSource didn't actually do any pooling 
>> itself, and that you needed another layer on top to manage a connection 
>> pool -- that seems to be how all previous revisions of 
>> JDBCConnectionPool worked, so I guess I wasn't alone in thinking this.  
>> But yes, BasicDataSource does seem to do pooling itself (confirmed by 
>> reading the source), so maybe your simpler version is a better idea.  It 
>> certainly works okay for me.
>>
>>            Thomas.
> 
> That's what I thought should have happened :). Can I suggest that this 
> revised version goes into CVS? Anyone got any objections?
> 
> Andy
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
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From td2 at sanger.ac.uk  Wed Jan 31 07:50:23 2007
From: td2 at sanger.ac.uk (Thomas Down)
Date: Wed, 31 Jan 2007 12:50:23 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <45C08B7A.3060102@ebi.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
	<45C0781B.7030304@ebi.ac.uk>
	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>
	<45C08639.7080600@ebi.ac.uk>
	<8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>
	<45C08B7A.3060102@ebi.ac.uk>
Message-ID: <F510F9CE-7B2F-4B0B-9DC3-6165BE4CA7FA@sanger.ac.uk>


On 31 Jan 2007, at 12:28, Andy Yates wrote:
>>
>> Hmmm, I was assuming that BasicDataSource didn't actually do any  
>> pooling
>> itself, and that you needed another layer on top to manage a  
>> connection
>> pool -- that seems to be how all previous revisions of
>> JDBCConnectionPool worked, so I guess I wasn't alone in thinking  
>> this.
>> But yes, BasicDataSource does seem to do pooling itself (confirmed by
>> reading the source), so maybe your simpler version is a better  
>> idea.  It
>> certainly works okay for me.
>>
>>            Thomas.
>
> That's what I thought should have happened :). Can I suggest that this
> revised version goes into CVS? Anyone got any objections?

The one problem I can think of is that this might break any code  
which relies on DataSource objects having reliable hashCode/equals.   
I've found one place where this might be a problem, in  
OntologySQL.getOntologySQL.  That's a deprecated class, so maybe it's  
not a big issue -- but it might be worth asking around.

           Thomas.

From ayates at ebi.ac.uk  Wed Jan 31 07:56:29 2007
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 31 Jan 2007 12:56:29 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <F510F9CE-7B2F-4B0B-9DC3-6165BE4CA7FA@sanger.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
	<45C0781B.7030304@ebi.ac.uk>
	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>
	<45C08639.7080600@ebi.ac.uk>
	<8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>
	<45C08B7A.3060102@ebi.ac.uk>
	<F510F9CE-7B2F-4B0B-9DC3-6165BE4CA7FA@sanger.ac.uk>
Message-ID: <45C091FD.3020501@ebi.ac.uk>



Thomas Down wrote:
> 
> On 31 Jan 2007, at 12:28, Andy Yates wrote:
>>>
>>> Hmmm, I was assuming that BasicDataSource didn't actually do any pooling
>>> itself, and that you needed another layer on top to manage a connection
>>> pool -- that seems to be how all previous revisions of
>>> JDBCConnectionPool worked, so I guess I wasn't alone in thinking this.
>>> But yes, BasicDataSource does seem to do pooling itself (confirmed by
>>> reading the source), so maybe your simpler version is a better idea.  It
>>> certainly works okay for me.
>>>
>>>            Thomas.
>>
>> That's what I thought should have happened :). Can I suggest that this
>> revised version goes into CVS? Anyone got any objections?
> 
> The one problem I can think of is that this might break any code which 
> relies on DataSource objects having reliable hashCode/equals.  I've 
> found one place where this might be a problem, in 
> OntologySQL.getOntologySQL.  That's a deprecated class, so maybe it's 
> not a big issue -- but it might be worth asking around.
> 
>           Thomas.

If this is a problem then there is nothing wrong I guess with 
subclassing BasicDataSource & implementing the hashcode & equals methods 
from there. BasicDataSource gives access to URI/password/username so it 
should be a very simple matter of generating the correct methods. I can 
do that as the submitted version if required

Andy

From holland at ebi.ac.uk  Wed Jan 31 08:07:58 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 31 Jan 2007 13:07:58 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <45C090A6.10909@ebi.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>	<45C0781B.7030304@ebi.ac.uk>	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>	<45C08639.7080600@ebi.ac.uk>	<8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>
	<45C08B7A.3060102@ebi.ac.uk> <45C08E4E.2050308@ebi.ac.uk>
	<45C090A6.10909@ebi.ac.uk>
Message-ID: <45C094AE.1030101@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

I've committed your changes Andy.

Thomas, I wouldn't worry about OntologySQL. It's highly deprecated and
not supported - the whole biojavax/Hibernate thing made that code redundant.

Richard.

Andy Yates wrote:
> Okay I've attached the fix here.
> 
> I just did this in a text editor but I believe that the imports are
> okay. If you can just do a quick scan as well to make sure I haven't
> deleted anything that was very important.
> 
> I'll get on to the helpdesk now as well :)
> 
> Andy
> 
> Richard Holland wrote:
> Andy could you make the change to your local copy of the source file and
> email the file to me, that way I can make sure I don't get it wrong when
> I commit it.
> 
> Richard.
> 
> PS. You should probably have your own CVS account - email the OBF
> helpdesk and ask for one, saying I told you to. :)
> 
> 
> Andy Yates wrote:
>>>> Thomas Down wrote:
>>>>> On 31 Jan 2007, at 12:06, Andy Yates wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Sorry I was meaning if that if that method just becomes:
>>>>>>
>>>>>> public static DataSource getDataSource(final String driver,
>>>>>>                                          final String url,
>>>>>>                                          final String user,
>>>>>>                                          final String pass)
>>>>>>     throws Exception {
>>>>>>
>>>>>>     BasicDataSource ds = new BasicDataSource();
>>>>>>     ds.setUrl(url);
>>>>>>     ds.setDriverClassName(driver);
>>>>>>     ds.setUsername(user);
>>>>>>     ds.setPassword(pass);
>>>>>>     // Set BasicDataSource properties such as maxActive and
>>>>>> maxIdle, as described in
>>>>>>     //
>>>>>> http://jakarta.apache.org/commons/dbcp/api/org/apache/commons/dbcp/BasicDataSource.html
>>>>>>
>>>>>>     ds.setMaxActive(10);
>>>>>>     ds.setMaxIdle(5);
>>>>>>     ds.setMaxWait(10000);
>>>>>>
>>>>>>     return ds;
>>>>>>   }
>>>>>>
>>>>>> Does that still work?
>>>>> Hmmm, I was assuming that BasicDataSource didn't actually do any
>>>>> pooling itself, and that you needed another layer on top to manage a
>>>>> connection pool -- that seems to be how all previous revisions of
>>>>> JDBCConnectionPool worked, so I guess I wasn't alone in thinking
>>>>> this.  But yes, BasicDataSource does seem to do pooling itself
>>>>> (confirmed by reading the source), so maybe your simpler version is
>>>>> a better idea.  It certainly works okay for me.
>>>>>
>>>>>            Thomas.
>>>> That's what I thought should have happened :). Can I suggest that
>>>> this revised version goes into CVS? Anyone got any objections?
>>>>
>>>> Andy
>>>> _______________________________________________
>>>> biojava-dev mailing list
>>>> biojava-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>>

> ------------------------------------------------------------------------

> /*
>  *                    BioJava development code
>  *
>  * This code may be freely distributed and modified under the
>  * terms of the GNU Lesser General Public Licence.  This should
>  * be distributed with the code.  If you do not have a copy,
>  * see:
>  *
>  *      http://www.gnu.org/copyleft/lesser.html
>  *
>  * Copyright for this code is held jointly by the individual
>  * authors.  These should be listed in @author doc comments.
>  *
>  * For more information on the BioJava project and its aims,
>  * or to join the biojava-l mailing list, visit the home page
>  * at:
>  *
>  *      http://www.biojava.org/
>  *
>  */
> package org.biojava.utils;

> import javax.sql.DataSource;

> import org.apache.commons.dbcp.BasicDataSource;
> import org.apache.commons.dbcp.PoolingDataSource;
> import org.apache.commons.pool.ObjectPool;

> /**
> * Returns a DataSource that implements connection pooling
> *
> * Uses Jakarta Commons DBCP and Pool packages.
> * See the description of the dbcp package at 
> * http://jakarta.apache.org/commons/dbcp/api/overview-summary.html#overview_description
> *
> * @author Simon Foote
> * @author Len Trigg
> */

> public class JDBCPooledDataSource {

>   public static DataSource getDataSource(final String driver, 
>                                          final String url,
>                                          final String user,
>                                          final String pass)
>     throws Exception {

>     BasicDataSource ds = new BasicDataSource();
>     ds.setUrl(url);
>     ds.setDriverClassName(driver);
>     ds.setUsername(user);
>     ds.setPassword(pass);
>     // Set BasicDataSource properties such as maxActive and maxIdle, as described in
>     // http://jakarta.apache.org/commons/dbcp/api/org/apache/commons/dbcp/BasicDataSource.html
>     ds.setMaxActive(10);
>     ds.setMaxIdle(5);
>     ds.setMaxWait(10000);

>     return dataSource;
>   }


>   // Adds simple equals and hashcode methods so that we can compare if
>   // two connections are to the same database. This will fail if the
>   // DataSource is redirected to another database etc (I doubt this is
>   // ever likely to be used).
>   /**
>    * @depercated This is no longer used in favor of {@link BasicDataSource}
>    * from DBCP
>    */
>   static class MyPoolingDataSource extends PoolingDataSource {
>     final String source;
>     public MyPoolingDataSource(ObjectPool connectionPool, String source) {
>       super(connectionPool);
>       this.source = source;
>     }
>     public boolean equals(Object o2) {
>       if ((o2 == null) || !(o2 instanceof MyPoolingDataSource)) {
>         return false;
>       }
>       MyPoolingDataSource b2 = (MyPoolingDataSource) o2;
>       return source.equals(b2.source);
>     }
>     public int hashCode() {
>       return source.hashCode();
>     }
>   }


>   public static void main(String[] args) {
>     try {
>       DataSource ds1 = getDataSource("org.hsqldb.jdbcDriver", "jdbc:hsqldb:/tmp/hsqldb/biosql", "sa", "");
>       DataSource ds2 = getDataSource("org.hsqldb.jdbcDriver", "jdbc:hsqldb:/tmp/hsqldb/biosql", "sa", "");
>       System.err.println(ds1);
>       System.err.println(ds2);
>       System.err.println(ds1.equals(ds2));
>     } catch (Exception e) {
>       e.printStackTrace();
>     }
>   }
> }
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From ayates at ebi.ac.uk  Wed Jan 31 08:25:12 2007
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 31 Jan 2007 13:25:12 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <45C094AE.1030101@ebi.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>	<45C0781B.7030304@ebi.ac.uk>	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>	<45C08639.7080600@ebi.ac.uk>	<8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>
	<45C08B7A.3060102@ebi.ac.uk> <45C08E4E.2050308@ebi.ac.uk>
	<45C090A6.10909@ebi.ac.uk> <45C094AE.1030101@ebi.ac.uk>
Message-ID: <45C098B8.7030107@ebi.ac.uk>

Cheers mate. If this hash/equals is a problem then this can be solved 
later on.

Richard Holland wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> I've committed your changes Andy.
> 
> Thomas, I wouldn't worry about OntologySQL. It's highly deprecated and
> not supported - the whole biojavax/Hibernate thing made that code redundant.
> 
> Richard.
> 
> Andy Yates wrote:
>> Okay I've attached the fix here.
>>
>> I just did this in a text editor but I believe that the imports are
>> okay. If you can just do a quick scan as well to make sure I haven't
>> deleted anything that was very important.
>>
>> I'll get on to the helpdesk now as well :)
>>
>> Andy
>>
>> Richard Holland wrote:
>> Andy could you make the change to your local copy of the source file and
>> email the file to me, that way I can make sure I don't get it wrong when
>> I commit it.
>>
>> Richard.
>>
>> PS. You should probably have your own CVS account - email the OBF
>> helpdesk and ask for one, saying I told you to. :)
>>
>>
>> Andy Yates wrote:
>>>>> Thomas Down wrote:
>>>>>> On 31 Jan 2007, at 12:06, Andy Yates wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> Sorry I was meaning if that if that method just becomes:
>>>>>>>
>>>>>>> public static DataSource getDataSource(final String driver,
>>>>>>>                                          final String url,
>>>>>>>                                          final String user,
>>>>>>>                                          final String pass)
>>>>>>>     throws Exception {
>>>>>>>
>>>>>>>     BasicDataSource ds = new BasicDataSource();
>>>>>>>     ds.setUrl(url);
>>>>>>>     ds.setDriverClassName(driver);
>>>>>>>     ds.setUsername(user);
>>>>>>>     ds.setPassword(pass);
>>>>>>>     // Set BasicDataSource properties such as maxActive and
>>>>>>> maxIdle, as described in
>>>>>>>     //
>>>>>>> http://jakarta.apache.org/commons/dbcp/api/org/apache/commons/dbcp/BasicDataSource.html
>>>>>>>
>>>>>>>     ds.setMaxActive(10);
>>>>>>>     ds.setMaxIdle(5);
>>>>>>>     ds.setMaxWait(10000);
>>>>>>>
>>>>>>>     return ds;
>>>>>>>   }
>>>>>>>
>>>>>>> Does that still work?
>>>>>> Hmmm, I was assuming that BasicDataSource didn't actually do any
>>>>>> pooling itself, and that you needed another layer on top to manage a
>>>>>> connection pool -- that seems to be how all previous revisions of
>>>>>> JDBCConnectionPool worked, so I guess I wasn't alone in thinking
>>>>>> this.  But yes, BasicDataSource does seem to do pooling itself
>>>>>> (confirmed by reading the source), so maybe your simpler version is
>>>>>> a better idea.  It certainly works okay for me.
>>>>>>
>>>>>>            Thomas.
>>>>> That's what I thought should have happened :). Can I suggest that
>>>>> this revised version goes into CVS? Anyone got any objections?
>>>>>
>>>>> Andy
>>>>> _______________________________________________
>>>>> biojava-dev mailing list
>>>>> biojava-dev at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>>>
> 
>> ------------------------------------------------------------------------
> 
>> /*
>>  *                    BioJava development code
>>  *
>>  * This code may be freely distributed and modified under the
>>  * terms of the GNU Lesser General Public Licence.  This should
>>  * be distributed with the code.  If you do not have a copy,
>>  * see:
>>  *
>>  *      http://www.gnu.org/copyleft/lesser.html
>>  *
>>  * Copyright for this code is held jointly by the individual
>>  * authors.  These should be listed in @author doc comments.
>>  *
>>  * For more information on the BioJava project and its aims,
>>  * or to join the biojava-l mailing list, visit the home page
>>  * at:
>>  *
>>  *      http://www.biojava.org/
>>  *
>>  */
>> package org.biojava.utils;
> 
>> import javax.sql.DataSource;
> 
>> import org.apache.commons.dbcp.BasicDataSource;
>> import org.apache.commons.dbcp.PoolingDataSource;
>> import org.apache.commons.pool.ObjectPool;
> 
>> /**
>> * Returns a DataSource that implements connection pooling
>> *
>> * Uses Jakarta Commons DBCP and Pool packages.
>> * See the description of the dbcp package at 
>> * http://jakarta.apache.org/commons/dbcp/api/overview-summary.html#overview_description
>> *
>> * @author Simon Foote
>> * @author Len Trigg
>> */
> 
>> public class JDBCPooledDataSource {
> 
>>   public static DataSource getDataSource(final String driver, 
>>                                          final String url,
>>                                          final String user,
>>                                          final String pass)
>>     throws Exception {
> 
>>     BasicDataSource ds = new BasicDataSource();
>>     ds.setUrl(url);
>>     ds.setDriverClassName(driver);
>>     ds.setUsername(user);
>>     ds.setPassword(pass);
>>     // Set BasicDataSource properties such as maxActive and maxIdle, as described in
>>     // http://jakarta.apache.org/commons/dbcp/api/org/apache/commons/dbcp/BasicDataSource.html
>>     ds.setMaxActive(10);
>>     ds.setMaxIdle(5);
>>     ds.setMaxWait(10000);
> 
>>     return dataSource;
>>   }
> 
> 
>>   // Adds simple equals and hashcode methods so that we can compare if
>>   // two connections are to the same database. This will fail if the
>>   // DataSource is redirected to another database etc (I doubt this is
>>   // ever likely to be used).
>>   /**
>>    * @depercated This is no longer used in favor of {@link BasicDataSource}
>>    * from DBCP
>>    */
>>   static class MyPoolingDataSource extends PoolingDataSource {
>>     final String source;
>>     public MyPoolingDataSource(ObjectPool connectionPool, String source) {
>>       super(connectionPool);
>>       this.source = source;
>>     }
>>     public boolean equals(Object o2) {
>>       if ((o2 == null) || !(o2 instanceof MyPoolingDataSource)) {
>>         return false;
>>       }
>>       MyPoolingDataSource b2 = (MyPoolingDataSource) o2;
>>       return source.equals(b2.source);
>>     }
>>     public int hashCode() {
>>       return source.hashCode();
>>     }
>>   }
> 
> 
>>   public static void main(String[] args) {
>>     try {
>>       DataSource ds1 = getDataSource("org.hsqldb.jdbcDriver", "jdbc:hsqldb:/tmp/hsqldb/biosql", "sa", "");
>>       DataSource ds2 = getDataSource("org.hsqldb.jdbcDriver", "jdbc:hsqldb:/tmp/hsqldb/biosql", "sa", "");
>>       System.err.println(ds1);
>>       System.err.println(ds2);
>>       System.err.println(ds1.equals(ds2));
>>     } catch (Exception e) {
>>       e.printStackTrace();
>>     }
>>   }
>> }
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> 
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From jburdick at keyfitz.org  Mon Jan 22 11:46:44 2007
From: jburdick at keyfitz.org (Josh Burdick)
Date: Mon, 22 Jan 2007 16:46:44 -0000
Subject: [Biojava-dev] reading a subsequence from a .nib file
Message-ID: <1169483375.5340.39.camel@localhost.localdomain>

  I wrote some code to read a chunk of DNA sequence from a file in Jim
Kent's blat ".nib" file format.  This is a simple format using four
bits/base.

  I didn't attach the code, to avoid spamming the whole list; but it,
and a (very crude!) JUnit test, are at

http://www.keyfitz.org/jburdick/read_nib_file_java/NibFile.java
http://www.keyfitz.org/jburdick/read_nib_file_java/NibFileTest.java

  You could use 2 bits/base, but then you can't have ambiguous bases.  4
bits/base seems like a reasonable compromise; plus sites that have
"blat" installed will need to have the .nib files on a server somewhere
anyway, and this way repeat-masking can be included, which may be
convenient.

  Also, it doesn't support writing a .nib file; again, presumably people
will be using Jim Kent's faToNib program to do that.

  It would need some tweaking to be included in BioJava, because it
returns a plain String of ACGT, instead of a PackedSequence object.
(Probably this would just involve rewriting the setupBuffer() and
addToBuffer() methods in the code.)  Also, the coordinate information
could come from a Range object.

  If similar code is already somewhere in BioJava, please ignore this;
but I couldn't find it with thirty seconds of Googling, so I figured it
hadn't been written...

Josh Burdick
programmer, Vivian Cheung's lab, Children's Hospital of Philadelphia
jburdick at keyfitz.org



From ayates at ebi.ac.uk  Wed Jan 31 07:50:53 2007
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 31 Jan 2007 12:50:53 -0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <45C08E4E.2050308@ebi.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>	<45C0781B.7030304@ebi.ac.uk>	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>	<45C08639.7080600@ebi.ac.uk>	<8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>
	<45C08B7A.3060102@ebi.ac.uk> <45C08E4E.2050308@ebi.ac.uk>
Message-ID: <45C090A6.10909@ebi.ac.uk>

Okay I've attached the fix here.

I just did this in a text editor but I believe that the imports are 
okay. If you can just do a quick scan as well to make sure I haven't 
deleted anything that was very important.

I'll get on to the helpdesk now as well :)

Andy

Richard Holland wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> Andy could you make the change to your local copy of the source file and
> email the file to me, that way I can make sure I don't get it wrong when
> I commit it.
> 
> Richard.
> 
> PS. You should probably have your own CVS account - email the OBF
> helpdesk and ask for one, saying I told you to. :)
> 
> 
> Andy Yates wrote:
>> Thomas Down wrote:
>>> On 31 Jan 2007, at 12:06, Andy Yates wrote:
>>>
>>>> Hi,
>>>>
>>>> Sorry I was meaning if that if that method just becomes:
>>>>
>>>> public static DataSource getDataSource(final String driver,
>>>>                                          final String url,
>>>>                                          final String user,
>>>>                                          final String pass)
>>>>     throws Exception {
>>>>
>>>>     BasicDataSource ds = new BasicDataSource();
>>>>     ds.setUrl(url);
>>>>     ds.setDriverClassName(driver);
>>>>     ds.setUsername(user);
>>>>     ds.setPassword(pass);
>>>>     // Set BasicDataSource properties such as maxActive and maxIdle, 
>>>> as described in
>>>>     // 
>>>> http://jakarta.apache.org/commons/dbcp/api/org/apache/commons/dbcp/BasicDataSource.html 
>>>>
>>>>     ds.setMaxActive(10);
>>>>     ds.setMaxIdle(5);
>>>>     ds.setMaxWait(10000);
>>>>
>>>>     return ds;
>>>>   }
>>>>
>>>> Does that still work?
>>> Hmmm, I was assuming that BasicDataSource didn't actually do any pooling 
>>> itself, and that you needed another layer on top to manage a connection 
>>> pool -- that seems to be how all previous revisions of 
>>> JDBCConnectionPool worked, so I guess I wasn't alone in thinking this.  
>>> But yes, BasicDataSource does seem to do pooling itself (confirmed by 
>>> reading the source), so maybe your simpler version is a better idea.  It 
>>> certainly works okay for me.
>>>
>>>            Thomas.
>> That's what I thought should have happened :). Can I suggest that this 
>> revised version goes into CVS? Anyone got any objections?
>>
>> Andy
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
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From zbhuang2005 at hotmail.com  Tue Jan  2 13:16:16 2007
From: zbhuang2005 at hotmail.com (Huang Zhibin)
Date: Tue, 02 Jan 2007 13:16:16 +0000
Subject: [Biojava-dev] how to run unittest in eclipse
Message-ID: <BAY7-F23C6E75109962FA246420CA5BA0@phx.gbl>

Dear all,
  First all,thanks for the contribution of BioJava.
  I downloaded the BioJava and compile apps, demos, tests and runtests 
using ant. It is ok. But when importing this project into eclipse, I do not 
know hot to runtests. For example, when clicking file of 
/tests/org.biojava.bio.alignment/FlexibleAlignmentTest.java, choose Run As 
| JUnit Test, it fails. Info in Console will be listed below.
  I know maybe it failed in the step of initialization, but I do now know 
how to solve it.
  Can someone who run junittest in JAVA IDE share the experience or give me 
some suggestions? I will appreciate it.
Best regards,
Zhibin

------------------------------
Info printed in Console:

org.biojava.bio.BioError: Unable to initialize DNATools
	at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:117)
	at 
org.biojava.bio.alignment.FlexibleAlignmentTest.parse(FlexibleAlignmentTest.java:74)

	at 
org.biojava.bio.alignment.FlexibleAlignmentTest.<clinit>(FlexibleAlignmentTest.java:46)

	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown 
Source)
	at java.lang.reflect.Constructor.newInstance(Unknown Source)
	at junit.framework.TestSuite.createTest(TestSuite.java:135)
	at junit.framework.TestSuite.addTestMethod(TestSuite.java:114)
	at junit.framework.TestSuite.<init>(TestSuite.java:75)
	at 
org.eclipse.jdt.internal.junit.runner.junit3.JUnit3TestLoader.getTest(JUnit3TestLoader.java:102)

	at 
org.eclipse.jdt.internal.junit.runner.junit3.JUnit3TestLoader.loadTests(JUnit3TestLoader.java:59)

	at 
org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:445)

	at 
org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:673)

	at 
org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:386)

	at 
org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:196)

Caused by: org.biojava.bio.BioError: Couldn't locate AlphabetManager.xml.  
This probably means that your biojava.jar file is corrupt or incorrectly 
built.
	at 
org.biojava.bio.symbol.AlphabetManager.<clinit>(AlphabetManager.java:148)
	at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:80)
	... 15 more
java.lang.NoClassDefFoundError
	at org.biojava.bio.seq.ProteinTools.<clinit>(ProteinTools.java:76)
	at 
org.biojava.bio.alignment.FlexibleAlignmentTest.parse(FlexibleAlignmentTest.java:76)


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From bugzilla-daemon at portal.open-bio.org  Wed Jan  3 16:55:12 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 3 Jan 2007 11:55:12 -0500
Subject: [Biojava-dev] [Bug 2175] New: IndexOutOfBoundsException still
	occurring on SCF.create(File file)
Message-ID: <bug-2175-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2175

           Summary: IndexOutOfBoundsException still occurring on
                    SCF.create(File file)
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: blocker
          Priority: P1
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: cristyn at broad.mit.edu


SCF.create(File file) is still broken. I'm using the 1.5-beta2 download. Here
is the stacktrace:

ava.lang.IndexOutOfBoundsException
        at java.io.FileInputStream.readBytes(Native Method)
        at java.io.FileInputStream.read(FileInputStream.java:199)
        at java.io.DataInputStream.read(DataInputStream.java:132)
        at org.biojava.bio.program.scf.SCF$Parser.parsePrivate(SCF.java:391)
        at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:349)
        at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:202)
        at org.biojava.bio.program.scf.SCF.load(SCF.java:145)
        at org.biojava.bio.program.scf.SCF.load(SCF.java:140)
        at org.biojava.bio.program.scf.SCF.create(SCF.java:126)


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From bugzilla-daemon at portal.open-bio.org  Wed Jan  3 16:56:15 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 3 Jan 2007 11:56:15 -0500
Subject: [Biojava-dev] [Bug 2175] IndexOutOfBoundsException still occurring
	on SCF.create(File file)
In-Reply-To: <bug-2175-485@http.bugzilla.open-bio.org/>
Message-ID: <200701031656.l03GuFcn015619@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2175


cristyn at broad.mit.edu changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |cristyn at broad.mit.edu




------- Comment #1 from cristyn at broad.mit.edu  2007-01-03 11:56 -------
java.lang.IndexOutOfBoundsException
        at java.io.FileInputStream.readBytes(Native Method)
        at java.io.FileInputStream.read(FileInputStream.java:199)
        at java.io.DataInputStream.read(DataInputStream.java:132)
        at org.biojava.bio.program.scf.SCF$Parser.parsePrivate(SCF.java:391)
        at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:349)
        at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:202)
        at org.biojava.bio.program.scf.SCF.load(SCF.java:145)
        at org.biojava.bio.program.scf.SCF.load(SCF.java:140)
        at org.biojava.bio.program.scf.SCF.create(SCF.java:126)

1.5-beta2 version of SCF class.


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From bugzilla-daemon at portal.open-bio.org  Wed Jan  3 17:13:54 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 3 Jan 2007 12:13:54 -0500
Subject: [Biojava-dev] [Bug 2175] IndexOutOfBoundsException still occurring
	on SCF.create(File file)
In-Reply-To: <bug-2175-485@http.bugzilla.open-bio.org/>
Message-ID: <200701031713.l03HDsoN016548@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2175


holland at ebi.ac.uk changed:

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




------- Comment #2 from holland at ebi.ac.uk  2007-01-03 12:13 -------
1) please check that your SCF file is version 2 or version 3. More recent
versions are not yet supported.

2) the exception occurs whilst parsing a PRIVATE block in your SCF file. The
block is supposed to specify its size in the header and its offset from the
start, then the parser uses this size to read exactly the right amount of data
from the right location. In your case it sounds like the header contains an
incorrect (too large) size or an incorrect (too late) offset, and so the parser
is attempting to read more data than is actually present at the given offset.
This would be a bug in the SCF file not the parser.

Please could you check the above and get back to me - the file itself would be
useful too.


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From mark.schreiber at novartis.com  Thu Jan  4 03:14:36 2007
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Thu, 4 Jan 2007 11:14:36 +0800
Subject: [Biojava-dev] nio for io?
Message-ID: <OF148E290B.B091F08E-ON48257259.001133E5-48257259.0011D10E@ah.novartis.com>

Hello -

I have been reading about the NIO api recently (very remiss of me to leave 
it this long). There seems to be potential for this to greatly speed up 
our parsers such as memory mapping etc, however ....

Our current Format objects want to see something like a BufferedReader. We 
would probably need to make an extension to the Format interface to use a 
FileChannel of some sort as input.

If I do something so naive as use the Channels utility to wrap a Channel 
into a BufferedReader I get no advantage (it's even a bit slower).

There has been some talk of Sun reprogramming normal java.io objects to 
use NIO internally, does anyone know if this has happened (if it has there 
is probably not much point in us looking into it much)?

Are there people more experienced with this API that can see some 
potential for it to improve parsing speed (probably the biggest 
bioinformatics bottleneck)? Comments greatly appreciated.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910



From heuermh at acm.org  Thu Jan  4 06:02:55 2007
From: heuermh at acm.org (Michael Heuer)
Date: Thu, 4 Jan 2007 01:02:55 -0500 (EST)
Subject: [Biojava-dev] nio for io?
In-Reply-To: <OF148E290B.B091F08E-ON48257259.001133E5-48257259.0011D10E@ah.novartis.com>
Message-ID: <Pine.GSO.4.44.0701040057380.7916-100000@shell3.shore.net>

Mark Schreiber wrote:

> There has been some talk of Sun reprogramming normal java.io objects to
> use NIO internally, does anyone know if this has happened (if it has there
> is probably not much point in us looking into it much)?

I seem to remember the jdk release notes around 1.5 saying this was the
case.

Very unscientifically,

$ grep nio jdk1.6.0/src/java/io/*.java
ByteArrayOutputStream.java:     * default character set. The {@linkplain
java.nio.charset.CharsetDecoder}
ByteArrayOutputStream.java:     * the specified {@link
java.nio.charset.Charset charsetName}. The length of
ByteArrayOutputStream.java:     * java.nio.charset.CharsetDecoder} class
should be used when more control
ByteArrayOutputStream.java:     *                   {@linkplain
java.nio.charset.Charset </code>charset<code>}
Console.java:import java.nio.charset.Charset;
Console.java:import sun.nio.cs.StreamDecoder;
Console.java:import sun.nio.cs.StreamEncoder;
Console.java:    * {@link java.io.Reader#read(java.nio.CharBuffer)
read(java.nio.CharBuffer)}
File.java:     * {@link java.nio.channels.FileLock FileLock}
File.java:     * {@link java.nio.channels.FileLock FileLock}
FileInputStream.java:import java.nio.channels.FileChannel;
FileInputStream.java:import sun.nio.ch.FileChannelImpl;
FileInputStream.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
FileInputStream.java:     * <p> The initial {@link
java.nio.channels.FileChannel#position()
FileOutputStream.java:import java.nio.channels.FileChannel;
FileOutputStream.java:import sun.nio.ch.FileChannelImpl;
FileOutputStream.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
FileOutputStream.java:     * <p> The initial {@link
java.nio.channels.FileChannel#position()
InputStreamReader.java:import java.nio.charset.Charset;
InputStreamReader.java:import java.nio.charset.CharsetDecoder;
InputStreamReader.java:import sun.nio.cs.StreamDecoder;
InputStreamReader.java: * java.nio.charset.Charset <code>charset</code>}.
The charset that it uses
InputStreamReader.java: * @see java.nio.charset.Charset
InputStreamReader.java:     *         {@link java.nio.charset.Charset
</code>charset<code>}
InputStreamReader.java:     * @see java.nio.charset.Charset
OutputStreamWriter.java:import java.nio.charset.Charset;
OutputStreamWriter.java:import java.nio.charset.CharsetEncoder;
OutputStreamWriter.java:import sun.nio.cs.StreamEncoder;
OutputStreamWriter.java: * java.nio.charset.Charset <code>charset</code>}.
The charset that it uses
OutputStreamWriter.java: * The {@linkplain
java.nio.charset.CharsetEncoder} class should be used when more
OutputStreamWriter.java: * @see java.nio.charset.Charset
OutputStreamWriter.java:     *         {@link java.nio.charset.Charset
</code>charset<code>}
OutputStreamWriter.java:     * @see java.nio.charset.Charset
PrintStream.java:     * {@linkplain
java.nio.charset.Charset#defaultCharset() default charset}
PrintStream.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintStream.java:     * java.nio.charset.Charset#defaultCharset() default
charset} for this
PrintStream.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintWriter.java:     * java.nio.charset.Charset#defaultCharset() default
charset} for this
PrintWriter.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintWriter.java:     * java.nio.charset.Charset#defaultCharset() default
charset} for this
PrintWriter.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
RandomAccessFile.java:import java.nio.channels.FileChannel;
RandomAccessFile.java:import sun.nio.ch.FileChannelImpl;
RandomAccessFile.java:     * java.nio.channels.FileChannel#force(boolean)
force(boolean)} method of
RandomAccessFile.java:     * the {@link java.nio.channels.FileChannel}
class, passing arguments of
RandomAccessFile.java:     * @see
java.nio.channels.FileChannel#force(boolean)
RandomAccessFile.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
RandomAccessFile.java:     * <p> The {@link
java.nio.channels.FileChannel#position()
Reader.java:    public int read(java.nio.CharBuffer target) throws
IOException {


$ grep nio jdk1.5.0_08/src/java/io/*.java
File.java:     * {@link java.nio.channels.FileLock FileLock}
File.java:     * {@link java.nio.channels.FileLock FileLock}
FileInputStream.java:import java.nio.channels.FileChannel;
FileInputStream.java:import sun.nio.ch.FileChannelImpl;
FileInputStream.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
FileInputStream.java:     * <p> The initial {@link
java.nio.channels.FileChannel#position()
FileOutputStream.java:import java.nio.channels.FileChannel;
FileOutputStream.java:import sun.nio.ch.FileChannelImpl;
FileOutputStream.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
FileOutputStream.java:     * <p> The initial {@link
java.nio.channels.FileChannel#position()
InputStreamReader.java:import java.nio.charset.Charset;
InputStreamReader.java:import java.nio.charset.CharsetDecoder;
InputStreamReader.java:import sun.nio.cs.StreamDecoder;
InputStreamReader.java: * java.nio.charset.Charset <code>charset</code>}.
The charset that it uses
InputStreamReader.java: * @see java.nio.charset.Charset
InputStreamReader.java:     *         {@link java.nio.charset.Charset
</code>charset<code>}
InputStreamReader.java:     * @see java.nio.charset.Charset
OutputStreamWriter.java:import java.nio.charset.Charset;
OutputStreamWriter.java:import java.nio.charset.CharsetEncoder;
OutputStreamWriter.java:import sun.nio.cs.StreamEncoder;
OutputStreamWriter.java: * java.nio.charset.Charset <code>charset</code>}.
The charset that it uses
OutputStreamWriter.java: * @see java.nio.charset.Charset
OutputStreamWriter.java:     *         {@link java.nio.charset.Charset
</code>charset<code>}
OutputStreamWriter.java:     * @see java.nio.charset.Charset
PrintStream.java:     * {@linkplain
java.nio.charset.Charset#defaultCharset default charset}
PrintStream.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintStream.java:     * java.nio.charset.Charset#defaultCharset default
charset} for this
PrintStream.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintWriter.java:     * java.nio.charset.Charset#defaultCharset default
charset} for this
PrintWriter.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintWriter.java:     * java.nio.charset.Charset#defaultCharset default
charset} for this
PrintWriter.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
RandomAccessFile.java:import java.nio.channels.FileChannel;
RandomAccessFile.java:import sun.nio.ch.FileChannelImpl;
RandomAccessFile.java:     * java.nio.channels.FileChannel#force(boolean)
force(boolean)} method of
RandomAccessFile.java:     * the {@link java.nio.channels.FileChannel}
class, passing arguments of
RandomAccessFile.java:     * @see
java.nio.channels.FileChannel#force(boolean)
RandomAccessFile.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
RandomAccessFile.java:     * <p> The {@link
java.nio.channels.FileChannel#position()
Reader.java:    public int read(java.nio.CharBuffer target) throws
IOException {

:)

   michael



From mark.schreiber at novartis.com  Thu Jan  4 06:26:51 2007
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Thu, 4 Jan 2007 14:26:51 +0800
Subject: [Biojava-dev] nio for io?
Message-ID: <OF19604BED.EC856085-ON48257259.00231D44-48257259.00236B25@ah.novartis.com>

OK , probably no gains to be made here then. Another good reason for 
people to upgrade to 1.5 or 1.6 if they have not already done so.

It may also explain why things slowed down when I used the converter in 
Channels. I was wrapping a Channel into something that already used one.

- Mark





Michael Heuer <heuermh at acm.org>
Sent by: biojava-dev-bounces at lists.open-bio.org
01/04/2007 02:02 PM

 
        To:     mark.schreiber at novartis.com
        cc:     biojava-dev at biojava.org
        Subject:        Re: [Biojava-dev] nio for io?


Mark Schreiber wrote:

> There has been some talk of Sun reprogramming normal java.io objects to
> use NIO internally, does anyone know if this has happened (if it has 
there
> is probably not much point in us looking into it much)?

I seem to remember the jdk release notes around 1.5 saying this was the
case.

Very unscientifically,

$ grep nio jdk1.6.0/src/java/io/*.java
ByteArrayOutputStream.java:     * default character set. The {@linkplain
java.nio.charset.CharsetDecoder}
ByteArrayOutputStream.java:     * the specified {@link
java.nio.charset.Charset charsetName}. The length of
ByteArrayOutputStream.java:     * java.nio.charset.CharsetDecoder} class
should be used when more control
ByteArrayOutputStream.java:     *                   {@linkplain
java.nio.charset.Charset </code>charset<code>}
Console.java:import java.nio.charset.Charset;
Console.java:import sun.nio.cs.StreamDecoder;
Console.java:import sun.nio.cs.StreamEncoder;
Console.java:    * {@link java.io.Reader#read(java.nio.CharBuffer)
read(java.nio.CharBuffer)}
File.java:     * {@link java.nio.channels.FileLock FileLock}
File.java:     * {@link java.nio.channels.FileLock FileLock}
FileInputStream.java:import java.nio.channels.FileChannel;
FileInputStream.java:import sun.nio.ch.FileChannelImpl;
FileInputStream.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
FileInputStream.java:     * <p> The initial {@link
java.nio.channels.FileChannel#position()
FileOutputStream.java:import java.nio.channels.FileChannel;
FileOutputStream.java:import sun.nio.ch.FileChannelImpl;
FileOutputStream.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
FileOutputStream.java:     * <p> The initial {@link
java.nio.channels.FileChannel#position()
InputStreamReader.java:import java.nio.charset.Charset;
InputStreamReader.java:import java.nio.charset.CharsetDecoder;
InputStreamReader.java:import sun.nio.cs.StreamDecoder;
InputStreamReader.java: * java.nio.charset.Charset <code>charset</code>}.
The charset that it uses
InputStreamReader.java: * @see java.nio.charset.Charset
InputStreamReader.java:     *         {@link java.nio.charset.Charset
</code>charset<code>}
InputStreamReader.java:     * @see java.nio.charset.Charset
OutputStreamWriter.java:import java.nio.charset.Charset;
OutputStreamWriter.java:import java.nio.charset.CharsetEncoder;
OutputStreamWriter.java:import sun.nio.cs.StreamEncoder;
OutputStreamWriter.java: * java.nio.charset.Charset <code>charset</code>}.
The charset that it uses
OutputStreamWriter.java: * The {@linkplain
java.nio.charset.CharsetEncoder} class should be used when more
OutputStreamWriter.java: * @see java.nio.charset.Charset
OutputStreamWriter.java:     *         {@link java.nio.charset.Charset
</code>charset<code>}
OutputStreamWriter.java:     * @see java.nio.charset.Charset
PrintStream.java:     * {@linkplain
java.nio.charset.Charset#defaultCharset() default charset}
PrintStream.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintStream.java:     * java.nio.charset.Charset#defaultCharset() default
charset} for this
PrintStream.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintWriter.java:     * java.nio.charset.Charset#defaultCharset() default
charset} for this
PrintWriter.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintWriter.java:     * java.nio.charset.Charset#defaultCharset() default
charset} for this
PrintWriter.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
RandomAccessFile.java:import java.nio.channels.FileChannel;
RandomAccessFile.java:import sun.nio.ch.FileChannelImpl;
RandomAccessFile.java:     * java.nio.channels.FileChannel#force(boolean)
force(boolean)} method of
RandomAccessFile.java:     * the {@link java.nio.channels.FileChannel}
class, passing arguments of
RandomAccessFile.java:     * @see
java.nio.channels.FileChannel#force(boolean)
RandomAccessFile.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
RandomAccessFile.java:     * <p> The {@link
java.nio.channels.FileChannel#position()
Reader.java:    public int read(java.nio.CharBuffer target) throws
IOException {


$ grep nio jdk1.5.0_08/src/java/io/*.java
File.java:     * {@link java.nio.channels.FileLock FileLock}
File.java:     * {@link java.nio.channels.FileLock FileLock}
FileInputStream.java:import java.nio.channels.FileChannel;
FileInputStream.java:import sun.nio.ch.FileChannelImpl;
FileInputStream.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
FileInputStream.java:     * <p> The initial {@link
java.nio.channels.FileChannel#position()
FileOutputStream.java:import java.nio.channels.FileChannel;
FileOutputStream.java:import sun.nio.ch.FileChannelImpl;
FileOutputStream.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
FileOutputStream.java:     * <p> The initial {@link
java.nio.channels.FileChannel#position()
InputStreamReader.java:import java.nio.charset.Charset;
InputStreamReader.java:import java.nio.charset.CharsetDecoder;
InputStreamReader.java:import sun.nio.cs.StreamDecoder;
InputStreamReader.java: * java.nio.charset.Charset <code>charset</code>}.
The charset that it uses
InputStreamReader.java: * @see java.nio.charset.Charset
InputStreamReader.java:     *         {@link java.nio.charset.Charset
</code>charset<code>}
InputStreamReader.java:     * @see java.nio.charset.Charset
OutputStreamWriter.java:import java.nio.charset.Charset;
OutputStreamWriter.java:import java.nio.charset.CharsetEncoder;
OutputStreamWriter.java:import sun.nio.cs.StreamEncoder;
OutputStreamWriter.java: * java.nio.charset.Charset <code>charset</code>}.
The charset that it uses
OutputStreamWriter.java: * @see java.nio.charset.Charset
OutputStreamWriter.java:     *         {@link java.nio.charset.Charset
</code>charset<code>}
OutputStreamWriter.java:     * @see java.nio.charset.Charset
PrintStream.java:     * {@linkplain
java.nio.charset.Charset#defaultCharset default charset}
PrintStream.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintStream.java:     * java.nio.charset.Charset#defaultCharset default
charset} for this
PrintStream.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintWriter.java:     * java.nio.charset.Charset#defaultCharset default
charset} for this
PrintWriter.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
PrintWriter.java:     * java.nio.charset.Charset#defaultCharset default
charset} for this
PrintWriter.java:     *         The name of a supported {@linkplain
java.nio.charset.Charset
RandomAccessFile.java:import java.nio.channels.FileChannel;
RandomAccessFile.java:import sun.nio.ch.FileChannelImpl;
RandomAccessFile.java:     * java.nio.channels.FileChannel#force(boolean)
force(boolean)} method of
RandomAccessFile.java:     * the {@link java.nio.channels.FileChannel}
class, passing arguments of
RandomAccessFile.java:     * @see
java.nio.channels.FileChannel#force(boolean)
RandomAccessFile.java:     * Returns the unique {@link
java.nio.channels.FileChannel FileChannel}
RandomAccessFile.java:     * <p> The {@link
java.nio.channels.FileChannel#position()
Reader.java:    public int read(java.nio.CharBuffer target) throws
IOException {

:)

   michael

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From bugzilla-daemon at portal.open-bio.org  Thu Jan  4 16:54:06 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 4 Jan 2007 11:54:06 -0500
Subject: [Biojava-dev] [Bug 2175] IndexOutOfBoundsException still occurring
	on SCF.create(File file)
In-Reply-To: <bug-2175-485@http.bugzilla.open-bio.org/>
Message-ID: <200701041654.l04Gs6NG014233@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2175


holland at ebi.ac.uk changed:

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




------- Comment #3 from holland at ebi.ac.uk  2007-01-04 11:54 -------
I've added a workaround to this in the head of CVS, but not in the beta
branches etc.

Basically I was right - the file given as an example has incorrect values in
its header data declaring that the private block is much bigger (835) than it
actually is (698). 

The workaround causes the parser to notice this and not attempt to read the
excess data. As the private block is not used anywhere inside the parser class
and is not visible to outside users, this should not affect anyone's code.


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From bugzilla-daemon at portal.open-bio.org  Fri Jan  5 10:16:02 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 5 Jan 2007 05:16:02 -0500
Subject: [Biojava-dev] [Bug 2177] New: Unclosed streams in
	org.biojava.bio.program.scf.SCF
Message-ID: <bug-2177-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2177

           Summary: Unclosed streams in org.biojava.bio.program.scf.SCF
           Product: BioJava
           Version: 1.4
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: major
          Priority: P2
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: keiranmraine at gmail.com


Hi,

There are problems in the following methods where the input streams have not
been closed.  This can cause a 'too many open files' os error when working
rapidly over large data sets.

org.biojava.bio.program.scf.SCF.load(File f)
- FileInputStream fin;

org.biojava.bio.program.scf.SCF.ParserFactory.parse(InputStream in, SCF out,
long initOffset)
 - DataInputStream din


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From bugzilla-daemon at portal.open-bio.org  Fri Jan  5 10:42:45 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 5 Jan 2007 05:42:45 -0500
Subject: [Biojava-dev] [Bug 2177] Unclosed streams in
	org.biojava.bio.program.scf.SCF
In-Reply-To: <bug-2177-485@http.bugzilla.open-bio.org/>
Message-ID: <200701051042.l05Agj4l030583@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2177





------- Comment #1 from andyyatz at gmail.com  2007-01-05 05:42 -------
(In reply to comment #0)
> Hi,
> 
> There are problems in the following methods where the input streams have not
> been closed.  This can cause a 'too many open files' os error when working
> rapidly over large data sets.
> 
> org.biojava.bio.program.scf.SCF.load(File f)
> - FileInputStream fin;
> 
> org.biojava.bio.program.scf.SCF.ParserFactory.parse(InputStream in, SCF out,
> long initOffset)
>  - DataInputStream din
> 

After a quick look at the source:

1). Yes SCF.load(File f) needs to be changed to:

protected void load(File f) throws IOException,
  UnsupportedChromatogramFormatException {
  FileInputStream fin = new FileInputStream(f);
  try {
    load(fin, 0);
  }
  finally {
    fin.close();
  }
}

Since this method opens the InputStream to the SCF file it has to be
responsible for closing the stream.

2). I don't think that parse(InputStream in, SCF out, long initOffset) should
be closing streams since it does not create them. It should be creating
method's responsibility to close these streams.


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From bugzilla-daemon at portal.open-bio.org  Fri Jan  5 10:55:32 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 5 Jan 2007 05:55:32 -0500
Subject: [Biojava-dev] [Bug 2177] Unclosed streams in
	org.biojava.bio.program.scf.SCF
In-Reply-To: <bug-2177-485@http.bugzilla.open-bio.org/>
Message-ID: <200701051055.l05AtWi4031158@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2177





------- Comment #2 from andyyatz at gmail.com  2007-01-05 05:55 -------
Created an attachment (id=535)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=535&action=view)
Patch for SCF class

First patch file I've created so sorry if it is wrong but I've tested the
patching process on my machine and it seems to work. Can someone please do a
quick compile with patch for me please?


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From bugzilla-daemon at portal.open-bio.org  Fri Jan  5 11:07:01 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 5 Jan 2007 06:07:01 -0500
Subject: [Biojava-dev] [Bug 2177] Unclosed streams in
	org.biojava.bio.program.scf.SCF
In-Reply-To: <bug-2177-485@http.bugzilla.open-bio.org/>
Message-ID: <200701051107.l05B71LE031749@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2177





------- Comment #3 from holland at ebi.ac.uk  2007-01-05 06:07 -------
I've tested and applied Andy's patch in CVS head. All seems to work nicely now.


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From bugzilla-daemon at portal.open-bio.org  Fri Jan  5 11:07:21 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 5 Jan 2007 06:07:21 -0500
Subject: [Biojava-dev] [Bug 2177] Unclosed streams in
	org.biojava.bio.program.scf.SCF
In-Reply-To: <bug-2177-485@http.bugzilla.open-bio.org/>
Message-ID: <200701051107.l05B7L8f031793@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2177


holland at ebi.ac.uk changed:

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




------- Comment #4 from holland at ebi.ac.uk  2007-01-05 06:07 -------
I've tested and applied Andy's patch in CVS head. All seems to work nicely now.


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From bugzilla-daemon at portal.open-bio.org  Fri Jan  5 11:10:07 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 5 Jan 2007 06:10:07 -0500
Subject: [Biojava-dev] [Bug 2177] Unclosed streams in
	org.biojava.bio.program.scf.SCF
In-Reply-To: <bug-2177-485@http.bugzilla.open-bio.org/>
Message-ID: <200701051110.l05BA7tM031932@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2177


keiranmraine at gmail.com changed:

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




------- Comment #5 from keiranmraine at gmail.com  2007-01-05 06:10 -------
I don't mean the input stream in the second method.  It's the DataInputStream
that should be closed here, see below.

public static void parse(InputStream in, SCF out, long initOffset)
        throws IOException, UnsupportedChromatogramFormatException {
  DataInputStream din;
  try {
    din = new DataInputStream(in);
    SCF.Parser parser = createParser(din, out, initOffset);
    parser.parse();
  }
  finally {
    din.close();
  }
}


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From bugzilla-daemon at portal.open-bio.org  Fri Jan  5 11:21:14 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 5 Jan 2007 06:21:14 -0500
Subject: [Biojava-dev] [Bug 2177] Unclosed streams in
	org.biojava.bio.program.scf.SCF
In-Reply-To: <bug-2177-485@http.bugzilla.open-bio.org/>
Message-ID: <200701051121.l05BLEXp032535@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2177


holland at ebi.ac.uk changed:

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




------- Comment #6 from holland at ebi.ac.uk  2007-01-05 06:21 -------
Publicly visible methods that accept InputStreams should never ever close them
- that is the responsibility of the caller. If the DataInputStream wrapping the
InputStream were closed, it would also close the InputStream, thus breaking
this contract. The DataInputStream will be implicitly closed when the caller
closes the original InputStream after calling the method in question.


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From bugzilla-daemon at portal.open-bio.org  Fri Jan  5 11:27:30 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 5 Jan 2007 06:27:30 -0500
Subject: [Biojava-dev] [Bug 2177] Unclosed streams in
	org.biojava.bio.program.scf.SCF
In-Reply-To: <bug-2177-485@http.bugzilla.open-bio.org/>
Message-ID: <200701051127.l05BRUUa000422@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2177





------- Comment #7 from keiranmraine at gmail.com  2007-01-05 06:27 -------
(In reply to comment #6)
> Publicly visible methods that accept InputStreams should never ever close them
> - that is the responsibility of the caller. If the DataInputStream wrapping the
> InputStream were closed, it would also close the InputStream, thus breaking
> this contract. The DataInputStream will be implicitly closed when the caller
> closes the original InputStream after calling the method in question.
> 

Ahhh, sorry sbout that, I did not realise that closing the DataInputStream
would close the InputStream.

Thanks


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From bugzilla-daemon at portal.open-bio.org  Tue Jan 16 17:35:53 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 16 Jan 2007 12:35:53 -0500
Subject: [Biojava-dev] [Bug 2186] New: ABIFparser never releases file
	resouce when generated with a File
Message-ID: <bug-2186-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2186

           Summary: ABIFparser never releases file resouce when generated
                    with a File
           Product: BioJava
           Version: 1.4
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: keiranmraine at gmail.com


Hi all,

I've detected a resource problem in the use of the following object constructor

org.biojava.bio.program.abi.ABIFParser(File f)

If you generate the parser in this manner the generated RandomAccessFile is
never closed and causes a resource leak.  The way the code is written I cannot
see an obvious place to close this, but there appears to be a simple fix in
that you can use the alternative method:

org.biojava.bio.program.abi.ABIFParser(InputStream in)

and control the closing outside of Biojava.

As I say I'm not sure at which point it's safe to close the stream in
ABIFParser but the File method could be removed??

Keiran


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 17 09:45:10 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 17 Jan 2007 04:45:10 -0500
Subject: [Biojava-dev] [Bug 2186] ABIFparser never releases file resouce
	when generated with a File
In-Reply-To: <bug-2186-485@http.bugzilla.open-bio.org/>
Message-ID: <200701170945.l0H9jAcx003234@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2186





------- Comment #1 from andyyatz at gmail.com  2007-01-17 04:45 -------
(In reply to comment #0)
> Hi all,
> 
> I've detected a resource problem in the use of the following object constructor
> 
> org.biojava.bio.program.abi.ABIFParser(File f)
> 
> If you generate the parser in this manner the generated RandomAccessFile is
> never closed and causes a resource leak.  The way the code is written I cannot
> see an obvious place to close this, but there appears to be a simple fix in
> that you can use the alternative method:
> 
> org.biojava.bio.program.abi.ABIFParser(InputStream in)
> 
> and control the closing outside of Biojava.
> 
> As I say I'm not sure at which point it's safe to close the stream in
> ABIFParser but the File method could be removed??
> 
> Keiran
> 

It would seem that way without a close method introduced into the parser which
then causes more problems. I would prefer a deprecation of the constructor to
warn future users that this is not the preferred way of creating an ABIFParser. 

Maybe an extension to this class should be a static builder method which takes
in a file, creates the required stream, passes out the finished object and
makes sure to clean up after itself. I don't know it this is possible as I've
only every gone into the guts of the ABI parser once.


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 17 10:41:45 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 17 Jan 2007 05:41:45 -0500
Subject: [Biojava-dev] [Bug 2186] ABIFparser never releases file resouce
	when generated with a File
In-Reply-To: <bug-2186-485@http.bugzilla.open-bio.org/>
Message-ID: <200701171041.l0HAfjR9005812@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2186


holland at ebi.ac.uk changed:

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




------- Comment #2 from holland at ebi.ac.uk  2007-01-17 05:41 -------
I found a way of changing it but it involved adding a method to the
ABIFParser.DataAccess interface. This does not affect anything internally to
BioJava but may affect user code - but I very much doubt anyone is using it.
Changes have been committed to the HEAD of biojava-live.


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 17 15:47:36 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 17 Jan 2007 10:47:36 -0500
Subject: [Biojava-dev] [Bug 2187] New: Stack trace printed:
	org.biojava.bio.program.scf.SCF$V3Parser.parseBases
Message-ID: <bug-2187-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2187

           Summary: Stack trace printed:
                    org.biojava.bio.program.scf.SCF$V3Parser.parseBases
           Product: BioJava
           Version: 1.4
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: keiranmraine at gmail.com


Hi,

Just a nicety for anyone using the class in programs for use by
non-programmers.

When catching the IllegalSymbolException the stack trace is printed in
org.biojava.bio.program.scf.SCF$V3Parser.parseBases.

I suggest that the UnsupportedChromatogramFormatException be extended to take
the Throwable and the 'ise.printStackTrace(System.err);' removed.

e.g.

catch (IllegalSymbolException ise) {
  ise.printStackTrace(System.err);
  throw new UnsupportedChromatogramFormatException("Base call decoding
failure");
}

BECOMES

catch (IllegalSymbolException ise) {
  throw new UnsupportedChromatogramFormatException("Base call decoding
failure", ise);
}


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 17 15:47:46 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 17 Jan 2007 10:47:46 -0500
Subject: [Biojava-dev] [Bug 2188] New: Stack trace printed:
	org.biojava.bio.program.scf.SCF$V3Parser.parseBases
Message-ID: <bug-2188-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2188

           Summary: Stack trace printed:
                    org.biojava.bio.program.scf.SCF$V3Parser.parseBases
           Product: BioJava
           Version: 1.4
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: keiranmraine at gmail.com


Hi,

Just a nicety for anyone using the class in programs for use by
non-programmers.

When catching the IllegalSymbolException the stack trace is printed in
org.biojava.bio.program.scf.SCF$V3Parser.parseBases.

I suggest that the UnsupportedChromatogramFormatException be extended to take
the Throwable and the 'ise.printStackTrace(System.err);' removed.

e.g.

catch (IllegalSymbolException ise) {
  ise.printStackTrace(System.err);
  throw new UnsupportedChromatogramFormatException("Base call decoding
failure");
}

BECOMES

catch (IllegalSymbolException ise) {
  throw new UnsupportedChromatogramFormatException("Base call decoding
failure", ise);
}


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 17 16:00:28 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 17 Jan 2007 11:00:28 -0500
Subject: [Biojava-dev] [Bug 2188] Stack trace printed:
	org.biojava.bio.program.scf.SCF$V3Parser.parseBases
In-Reply-To: <bug-2188-485@http.bugzilla.open-bio.org/>
Message-ID: <200701171600.l0HG0S0X030332@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2188


holland at ebi.ac.uk changed:

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




------- Comment #1 from holland at ebi.ac.uk  2007-01-17 11:00 -------


*** This bug has been marked as a duplicate of 2187 ***


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 17 16:00:32 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 17 Jan 2007 11:00:32 -0500
Subject: [Biojava-dev] [Bug 2187] Stack trace printed:
	org.biojava.bio.program.scf.SCF$V3Parser.parseBases
In-Reply-To: <bug-2187-485@http.bugzilla.open-bio.org/>
Message-ID: <200701171600.l0HG0WRv030352@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2187





------- Comment #1 from holland at ebi.ac.uk  2007-01-17 11:00 -------
*** Bug 2188 has been marked as a duplicate of this bug. ***


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From bugzilla-daemon at portal.open-bio.org  Wed Jan 17 16:03:22 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 17 Jan 2007 11:03:22 -0500
Subject: [Biojava-dev] [Bug 2187] Stack trace printed:
	org.biojava.bio.program.scf.SCF$V3Parser.parseBases
In-Reply-To: <bug-2187-485@http.bugzilla.open-bio.org/>
Message-ID: <200701171603.l0HG3MZU030882@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2187


holland at ebi.ac.uk changed:

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




------- Comment #2 from holland at ebi.ac.uk  2007-01-17 11:03 -------
I've made the change as suggested. Committed to CVS biojava-live HEAD.


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From holland at ebi.ac.uk  Fri Jan 19 15:54:45 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Fri, 19 Jan 2007 15:54:45 -0000
Subject: [Biojava-dev] SimpleGFFRecord
In-Reply-To: <200612201658.02312.tamir@imp.univie.ac.at>
References: <200612201658.02312.tamir@imp.univie.ac.at>
Message-ID: <458963F3.9020706@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Thanks for pointing this out. I have fixed it on the HEAD branch of CVS.

cheers,
Richard

Ido M. Tamir wrote:
> 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);
>   }
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
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Version: GnuPG v1.4.2.2 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFFiWPy4C5LeMEKA/QRAmJWAJ9jmAvPhQYF0YlJEYye7/XdPa7NhgCbBI5t
lImvTgNuqgd6/RukpFd4Pik=
=y7hf
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From ayates at ebi.ac.uk  Fri Jan 19 16:18:05 2007
From: ayates at ebi.ac.uk (Andy Yates)
Date: Fri, 19 Jan 2007 16:18:05 -0000
Subject: [Biojava-dev] how to run unittest in eclipse
In-Reply-To: <BAY7-F23C6E75109962FA246420CA5BA0@phx.gbl>
References: <BAY7-F23C6E75109962FA246420CA5BA0@phx.gbl>
Message-ID: <459A68DE.4020506@ebi.ac.uk>

Hi,

This sounds like a problem more with bad project setup where Eclipse has 
not been told where the resources directory is located.

In eclipse right click on the project and go to:

Build Path -> Configure Build Path...

Click on the source tab and then click on the button Add Folder. Select 
the resources directory from the root of the BioJava project and then 
click ok.

If everything has gone okay when you now run the test the Eclipse JUnit 
runner should pick up on the resources classpath and you should have a 
bit more luck with them.

Andy Yates

Huang Zhibin wrote:
> Dear all,
>  First all,thanks for the contribution of BioJava.
>  I downloaded the BioJava and compile apps, demos, tests and runtests 
> using ant. It is ok. But when importing this project into eclipse, I do 
> not know hot to runtests. For example, when clicking file of 
> /tests/org.biojava.bio.alignment/FlexibleAlignmentTest.java, choose Run 
> As | JUnit Test, it fails. Info in Console will be listed below.
>  I know maybe it failed in the step of initialization, but I do now know 
> how to solve it.
>  Can someone who run junittest in JAVA IDE share the experience or give 
> me some suggestions? I will appreciate it.
> Best regards,
> Zhibin
> 
> ------------------------------
> Info printed in Console:
> 
> org.biojava.bio.BioError: Unable to initialize DNATools
>     at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:117)
>     at 
> org.biojava.bio.alignment.FlexibleAlignmentTest.parse(FlexibleAlignmentTest.java:74) 
> 
> 
>     at 
> org.biojava.bio.alignment.FlexibleAlignmentTest.<clinit>(FlexibleAlignmentTest.java:46) 
> 
> 
>     at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native 
> Method)
>     at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown 
> Source)
>     at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown 
> Source)
>     at java.lang.reflect.Constructor.newInstance(Unknown Source)
>     at junit.framework.TestSuite.createTest(TestSuite.java:135)
>     at junit.framework.TestSuite.addTestMethod(TestSuite.java:114)
>     at junit.framework.TestSuite.<init>(TestSuite.java:75)
>     at 
> org.eclipse.jdt.internal.junit.runner.junit3.JUnit3TestLoader.getTest(JUnit3TestLoader.java:102) 
> 
> 
>     at 
> org.eclipse.jdt.internal.junit.runner.junit3.JUnit3TestLoader.loadTests(JUnit3TestLoader.java:59) 
> 
> 
>     at 
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:445) 
> 
> 
>     at 
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:673) 
> 
> 
>     at 
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:386) 
> 
> 
>     at 
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:196) 
> 
> 
> Caused by: org.biojava.bio.BioError: Couldn't locate 
> AlphabetManager.xml.  This probably means that your biojava.jar file is 
> corrupt or incorrectly built.
>     at 
> org.biojava.bio.symbol.AlphabetManager.<clinit>(AlphabetManager.java:148)
>     at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:80)
>     ... 15 more
> java.lang.NoClassDefFoundError
>     at org.biojava.bio.seq.ProteinTools.<clinit>(ProteinTools.java:76)
>     at 
> org.biojava.bio.alignment.FlexibleAlignmentTest.parse(FlexibleAlignmentTest.java:76) 
> 
> 
> 
> _________________________________________________________________
> ??????????,??? MSN Messenger:  http://messenger.msn.com/cn 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev


From td2 at sanger.ac.uk  Wed Jan 31 09:53:21 2007
From: td2 at sanger.ac.uk (Thomas Down)
Date: Wed, 31 Jan 2007 09:53:21 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
Message-ID: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>

Hi,

A few weeks ago, this patch removed a couple of apparently-redundant  
lines from JDBCPooledDataSource:

               http://code.open-bio.org/cgi/viewcvs.cgi/biojava-live/ 
src/org/biojava/utils/JDBCPooledDataSource.java.diff? 
r1=1.2&r2=1.3&cvsroot=biojava

This change causes at least some DataSource objects created using  
this class to fail with a NullPointerException the first time a  
connection is actually requested.  Using biojava-ensembl to access an  
Ensembl MySQL database demonstrates this problem consistently.   
Reverting to revision 1.2 of JDBCPooledDataSource.java solves the  
problem.

It looks like the PoolableConnectionFactory constructor has a side  
effect of registering the factory with the specified ObjectPool.   
This side effect doesn't seem to be documented particularly clearly,  
but the example code towards the bottom of:

           http://jakarta.apache.org/commons/dbcp/apidocs/org/apache/ 
commons/dbcp/package-summary.html#package_description

seems to rely on this behavior.


Would it be possible to roll this source file back to revision 1.2?   
Or, alternatively, is there someone who can set me up with commit  
access on the new CVS server (I think I still have an account there,  
but my password doesn't work since the server move).

Thanks,

                Thomas.


From holland at ebi.ac.uk  Wed Jan 31 11:04:05 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 31 Jan 2007 11:04:05 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
Message-ID: <45C077A5.4070706@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi Thomas. I have made the change on Head as you have requested.

cheers,
Richard.

Thomas Down wrote:
> Hi,
> 
> A few weeks ago, this patch removed a couple of apparently-redundant  
> lines from JDBCPooledDataSource:
> 
>                http://code.open-bio.org/cgi/viewcvs.cgi/biojava-live/ 
> src/org/biojava/utils/JDBCPooledDataSource.java.diff? 
> r1=1.2&r2=1.3&cvsroot=biojava
> 
> This change causes at least some DataSource objects created using  
> this class to fail with a NullPointerException the first time a  
> connection is actually requested.  Using biojava-ensembl to access an  
> Ensembl MySQL database demonstrates this problem consistently.   
> Reverting to revision 1.2 of JDBCPooledDataSource.java solves the  
> problem.
> 
> It looks like the PoolableConnectionFactory constructor has a side  
> effect of registering the factory with the specified ObjectPool.   
> This side effect doesn't seem to be documented particularly clearly,  
> but the example code towards the bottom of:
> 
>            http://jakarta.apache.org/commons/dbcp/apidocs/org/apache/ 
> commons/dbcp/package-summary.html#package_description
> 
> seems to rely on this behavior.
> 
> 
> Would it be possible to roll this source file back to revision 1.2?   
> Or, alternatively, is there someone who can set me up with commit  
> access on the new CVS server (I think I still have an account there,  
> but my password doesn't work since the server move).
> 
> Thanks,
> 
>                 Thomas.
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
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Version: GnuPG v1.4.2.2 (GNU/Linux)
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Lt0ZjTmBS2K+JGc3TF4R9Qg=
=kaAs
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From ayates at ebi.ac.uk  Wed Jan 31 11:06:03 2007
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 31 Jan 2007 11:06:03 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
Message-ID: <45C0781B.7030304@ebi.ac.uk>

Hi,

I would say that this class' method is trying to do too much. We have a 
method which is creating a BasicDataSource then not bothering to return 
it in favour of a custom one which implements a hashcode & equals 
method. Can you try your test case when it returns the BasicDataSource & 
not the custom one and see if that works please?

Thanks,

Andy Yates

Thomas Down wrote:
> Hi,
> 
> A few weeks ago, this patch removed a couple of apparently-redundant  
> lines from JDBCPooledDataSource:
> 
>                http://code.open-bio.org/cgi/viewcvs.cgi/biojava-live/ 
> src/org/biojava/utils/JDBCPooledDataSource.java.diff? 
> r1=1.2&r2=1.3&cvsroot=biojava
> 
> This change causes at least some DataSource objects created using  
> this class to fail with a NullPointerException the first time a  
> connection is actually requested.  Using biojava-ensembl to access an  
> Ensembl MySQL database demonstrates this problem consistently.   
> Reverting to revision 1.2 of JDBCPooledDataSource.java solves the  
> problem.
> 
> It looks like the PoolableConnectionFactory constructor has a side  
> effect of registering the factory with the specified ObjectPool.   
> This side effect doesn't seem to be documented particularly clearly,  
> but the example code towards the bottom of:
> 
>            http://jakarta.apache.org/commons/dbcp/apidocs/org/apache/ 
> commons/dbcp/package-summary.html#package_description
> 
> seems to rely on this behavior.
> 
> 
> Would it be possible to roll this source file back to revision 1.2?   
> Or, alternatively, is there someone who can set me up with commit  
> access on the new CVS server (I think I still have an account there,  
> but my password doesn't work since the server move).
> 
> Thanks,
> 
>                 Thomas.
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev


From td2 at sanger.ac.uk  Wed Jan 31 11:59:31 2007
From: td2 at sanger.ac.uk (Thomas Down)
Date: Wed, 31 Jan 2007 11:59:31 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <45C0781B.7030304@ebi.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
	<45C0781B.7030304@ebi.ac.uk>
Message-ID: <5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>


On 31 Jan 2007, at 11:06, Andy Yates wrote:

> Hi,
>
> I would say that this class' method is trying to do too much. We  
> have a
> method which is creating a BasicDataSource then not bothering to  
> return
> it in favour of a custom one which implements a hashcode & equals
> method. Can you try your test case when it returns the  
> BasicDataSource &
> not the custom one and see if that works please?

Patching the current revision to return a PoolingDataSource (I assume  
that's what you meant) rather than a MyPoolingDataSource works fine.   
However, patching revision 1.3 the same way does not work.  The  
problem I reported is definitely orthogonal to the question of  
exactly which type of PoolingDataSource gets returned.

I'm not sure what the original rationale was for returning the custom  
PoolingDataSource subclass -- but I can't really see how it's going  
to do any harm.

            Thomas.


From ayates at ebi.ac.uk  Wed Jan 31 12:06:17 2007
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 31 Jan 2007 12:06:17 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
	<45C0781B.7030304@ebi.ac.uk>
	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>
Message-ID: <45C08639.7080600@ebi.ac.uk>

Hi,

Sorry I was meaning if that if that method just becomes:

public static DataSource getDataSource(final String driver,
                                          final String url,
                                          final String user,
                                          final String pass)
     throws Exception {

     BasicDataSource ds = new BasicDataSource();
     ds.setUrl(url);
     ds.setDriverClassName(driver);
     ds.setUsername(user);
     ds.setPassword(pass);
     // Set BasicDataSource properties such as maxActive and maxIdle, as 
described in
     // 
http://jakarta.apache.org/commons/dbcp/api/org/apache/commons/dbcp/BasicDataSource.html
     ds.setMaxActive(10);
     ds.setMaxIdle(5);
     ds.setMaxWait(10000);

     return ds;
   }

Does that still work?

I think the original rationale was to ensure that any two datasources do 
actually point to the same resource. However this seems a bit too much 
defensive programming & I don't know why anyone would program themselves 
into a situation where this is required.

Andy

Thomas Down wrote:
> 
> On 31 Jan 2007, at 11:06, Andy Yates wrote:
> 
>> Hi,
>>
>> I would say that this class' method is trying to do too much. We have a
>> method which is creating a BasicDataSource then not bothering to return
>> it in favour of a custom one which implements a hashcode & equals
>> method. Can you try your test case when it returns the BasicDataSource &
>> not the custom one and see if that works please?
> 
> Patching the current revision to return a PoolingDataSource (I assume 
> that's what you meant) rather than a MyPoolingDataSource works fine.  
> However, patching revision 1.3 the same way does not work.  The problem 
> I reported is definitely orthogonal to the question of exactly which 
> type of PoolingDataSource gets returned.
> 
> I'm not sure what the original rationale was for returning the custom 
> PoolingDataSource subclass -- but I can't really see how it's going to 
> do any harm.
> 
>            Thomas.


From td2 at sanger.ac.uk  Wed Jan 31 12:21:10 2007
From: td2 at sanger.ac.uk (Thomas Down)
Date: Wed, 31 Jan 2007 12:21:10 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <45C08639.7080600@ebi.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
	<45C0781B.7030304@ebi.ac.uk>
	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>
	<45C08639.7080600@ebi.ac.uk>
Message-ID: <8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>


On 31 Jan 2007, at 12:06, Andy Yates wrote:

> Hi,
>
> Sorry I was meaning if that if that method just becomes:
>
> public static DataSource getDataSource(final String driver,
>                                          final String url,
>                                          final String user,
>                                          final String pass)
>     throws Exception {
>
>     BasicDataSource ds = new BasicDataSource();
>     ds.setUrl(url);
>     ds.setDriverClassName(driver);
>     ds.setUsername(user);
>     ds.setPassword(pass);
>     // Set BasicDataSource properties such as maxActive and  
> maxIdle, as described in
>     // http://jakarta.apache.org/commons/dbcp/api/org/apache/ 
> commons/dbcp/BasicDataSource.html
>     ds.setMaxActive(10);
>     ds.setMaxIdle(5);
>     ds.setMaxWait(10000);
>
>     return ds;
>   }
>
> Does that still work?

Hmmm, I was assuming that BasicDataSource didn't actually do any  
pooling itself, and that you needed another layer on top to manage a  
connection pool -- that seems to be how all previous revisions of  
JDBCConnectionPool worked, so I guess I wasn't alone in thinking  
this.  But yes, BasicDataSource does seem to do pooling itself  
(confirmed by reading the source), so maybe your simpler version is a  
better idea.  It certainly works okay for me.

            Thomas.


From ayates at ebi.ac.uk  Wed Jan 31 12:28:42 2007
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 31 Jan 2007 12:28:42 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
	<45C0781B.7030304@ebi.ac.uk>
	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>
	<45C08639.7080600@ebi.ac.uk>
	<8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>
Message-ID: <45C08B7A.3060102@ebi.ac.uk>



Thomas Down wrote:
> 
> On 31 Jan 2007, at 12:06, Andy Yates wrote:
> 
>> Hi,
>>
>> Sorry I was meaning if that if that method just becomes:
>>
>> public static DataSource getDataSource(final String driver,
>>                                          final String url,
>>                                          final String user,
>>                                          final String pass)
>>     throws Exception {
>>
>>     BasicDataSource ds = new BasicDataSource();
>>     ds.setUrl(url);
>>     ds.setDriverClassName(driver);
>>     ds.setUsername(user);
>>     ds.setPassword(pass);
>>     // Set BasicDataSource properties such as maxActive and maxIdle, 
>> as described in
>>     // 
>> http://jakarta.apache.org/commons/dbcp/api/org/apache/commons/dbcp/BasicDataSource.html 
>>
>>     ds.setMaxActive(10);
>>     ds.setMaxIdle(5);
>>     ds.setMaxWait(10000);
>>
>>     return ds;
>>   }
>>
>> Does that still work?
> 
> Hmmm, I was assuming that BasicDataSource didn't actually do any pooling 
> itself, and that you needed another layer on top to manage a connection 
> pool -- that seems to be how all previous revisions of 
> JDBCConnectionPool worked, so I guess I wasn't alone in thinking this.  
> But yes, BasicDataSource does seem to do pooling itself (confirmed by 
> reading the source), so maybe your simpler version is a better idea.  It 
> certainly works okay for me.
> 
>            Thomas.

That's what I thought should have happened :). Can I suggest that this 
revised version goes into CVS? Anyone got any objections?

Andy


From holland at ebi.ac.uk  Wed Jan 31 12:40:46 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 31 Jan 2007 12:40:46 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <45C08B7A.3060102@ebi.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>	<45C0781B.7030304@ebi.ac.uk>	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>	<45C08639.7080600@ebi.ac.uk>	<8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>
	<45C08B7A.3060102@ebi.ac.uk>
Message-ID: <45C08E4E.2050308@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Andy could you make the change to your local copy of the source file and
email the file to me, that way I can make sure I don't get it wrong when
I commit it.

Richard.

PS. You should probably have your own CVS account - email the OBF
helpdesk and ask for one, saying I told you to. :)


Andy Yates wrote:
> 
> Thomas Down wrote:
>> On 31 Jan 2007, at 12:06, Andy Yates wrote:
>>
>>> Hi,
>>>
>>> Sorry I was meaning if that if that method just becomes:
>>>
>>> public static DataSource getDataSource(final String driver,
>>>                                          final String url,
>>>                                          final String user,
>>>                                          final String pass)
>>>     throws Exception {
>>>
>>>     BasicDataSource ds = new BasicDataSource();
>>>     ds.setUrl(url);
>>>     ds.setDriverClassName(driver);
>>>     ds.setUsername(user);
>>>     ds.setPassword(pass);
>>>     // Set BasicDataSource properties such as maxActive and maxIdle, 
>>> as described in
>>>     // 
>>> http://jakarta.apache.org/commons/dbcp/api/org/apache/commons/dbcp/BasicDataSource.html 
>>>
>>>     ds.setMaxActive(10);
>>>     ds.setMaxIdle(5);
>>>     ds.setMaxWait(10000);
>>>
>>>     return ds;
>>>   }
>>>
>>> Does that still work?
>> Hmmm, I was assuming that BasicDataSource didn't actually do any pooling 
>> itself, and that you needed another layer on top to manage a connection 
>> pool -- that seems to be how all previous revisions of 
>> JDBCConnectionPool worked, so I guess I wasn't alone in thinking this.  
>> But yes, BasicDataSource does seem to do pooling itself (confirmed by 
>> reading the source), so maybe your simpler version is a better idea.  It 
>> certainly works okay for me.
>>
>>            Thomas.
> 
> That's what I thought should have happened :). Can I suggest that this 
> revised version goes into CVS? Anyone got any objections?
> 
> Andy
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
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From td2 at sanger.ac.uk  Wed Jan 31 12:50:23 2007
From: td2 at sanger.ac.uk (Thomas Down)
Date: Wed, 31 Jan 2007 12:50:23 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <45C08B7A.3060102@ebi.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
	<45C0781B.7030304@ebi.ac.uk>
	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>
	<45C08639.7080600@ebi.ac.uk>
	<8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>
	<45C08B7A.3060102@ebi.ac.uk>
Message-ID: <F510F9CE-7B2F-4B0B-9DC3-6165BE4CA7FA@sanger.ac.uk>


On 31 Jan 2007, at 12:28, Andy Yates wrote:
>>
>> Hmmm, I was assuming that BasicDataSource didn't actually do any  
>> pooling
>> itself, and that you needed another layer on top to manage a  
>> connection
>> pool -- that seems to be how all previous revisions of
>> JDBCConnectionPool worked, so I guess I wasn't alone in thinking  
>> this.
>> But yes, BasicDataSource does seem to do pooling itself (confirmed by
>> reading the source), so maybe your simpler version is a better  
>> idea.  It
>> certainly works okay for me.
>>
>>            Thomas.
>
> That's what I thought should have happened :). Can I suggest that this
> revised version goes into CVS? Anyone got any objections?

The one problem I can think of is that this might break any code  
which relies on DataSource objects having reliable hashCode/equals.   
I've found one place where this might be a problem, in  
OntologySQL.getOntologySQL.  That's a deprecated class, so maybe it's  
not a big issue -- but it might be worth asking around.

           Thomas.


From ayates at ebi.ac.uk  Wed Jan 31 12:56:29 2007
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 31 Jan 2007 12:56:29 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <F510F9CE-7B2F-4B0B-9DC3-6165BE4CA7FA@sanger.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>
	<45C0781B.7030304@ebi.ac.uk>
	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>
	<45C08639.7080600@ebi.ac.uk>
	<8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>
	<45C08B7A.3060102@ebi.ac.uk>
	<F510F9CE-7B2F-4B0B-9DC3-6165BE4CA7FA@sanger.ac.uk>
Message-ID: <45C091FD.3020501@ebi.ac.uk>



Thomas Down wrote:
> 
> On 31 Jan 2007, at 12:28, Andy Yates wrote:
>>>
>>> Hmmm, I was assuming that BasicDataSource didn't actually do any pooling
>>> itself, and that you needed another layer on top to manage a connection
>>> pool -- that seems to be how all previous revisions of
>>> JDBCConnectionPool worked, so I guess I wasn't alone in thinking this.
>>> But yes, BasicDataSource does seem to do pooling itself (confirmed by
>>> reading the source), so maybe your simpler version is a better idea.  It
>>> certainly works okay for me.
>>>
>>>            Thomas.
>>
>> That's what I thought should have happened :). Can I suggest that this
>> revised version goes into CVS? Anyone got any objections?
> 
> The one problem I can think of is that this might break any code which 
> relies on DataSource objects having reliable hashCode/equals.  I've 
> found one place where this might be a problem, in 
> OntologySQL.getOntologySQL.  That's a deprecated class, so maybe it's 
> not a big issue -- but it might be worth asking around.
> 
>           Thomas.

If this is a problem then there is nothing wrong I guess with 
subclassing BasicDataSource & implementing the hashcode & equals methods 
from there. BasicDataSource gives access to URI/password/username so it 
should be a very simple matter of generating the correct methods. I can 
do that as the submitted version if required

Andy


From holland at ebi.ac.uk  Wed Jan 31 13:07:58 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Wed, 31 Jan 2007 13:07:58 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <45C090A6.10909@ebi.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>	<45C0781B.7030304@ebi.ac.uk>	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>	<45C08639.7080600@ebi.ac.uk>	<8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>
	<45C08B7A.3060102@ebi.ac.uk> <45C08E4E.2050308@ebi.ac.uk>
	<45C090A6.10909@ebi.ac.uk>
Message-ID: <45C094AE.1030101@ebi.ac.uk>

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I've committed your changes Andy.

Thomas, I wouldn't worry about OntologySQL. It's highly deprecated and
not supported - the whole biojavax/Hibernate thing made that code redundant.

Richard.

Andy Yates wrote:
> Okay I've attached the fix here.
> 
> I just did this in a text editor but I believe that the imports are
> okay. If you can just do a quick scan as well to make sure I haven't
> deleted anything that was very important.
> 
> I'll get on to the helpdesk now as well :)
> 
> Andy
> 
> Richard Holland wrote:
> Andy could you make the change to your local copy of the source file and
> email the file to me, that way I can make sure I don't get it wrong when
> I commit it.
> 
> Richard.
> 
> PS. You should probably have your own CVS account - email the OBF
> helpdesk and ask for one, saying I told you to. :)
> 
> 
> Andy Yates wrote:
>>>> Thomas Down wrote:
>>>>> On 31 Jan 2007, at 12:06, Andy Yates wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Sorry I was meaning if that if that method just becomes:
>>>>>>
>>>>>> public static DataSource getDataSource(final String driver,
>>>>>>                                          final String url,
>>>>>>                                          final String user,
>>>>>>                                          final String pass)
>>>>>>     throws Exception {
>>>>>>
>>>>>>     BasicDataSource ds = new BasicDataSource();
>>>>>>     ds.setUrl(url);
>>>>>>     ds.setDriverClassName(driver);
>>>>>>     ds.setUsername(user);
>>>>>>     ds.setPassword(pass);
>>>>>>     // Set BasicDataSource properties such as maxActive and
>>>>>> maxIdle, as described in
>>>>>>     //
>>>>>> http://jakarta.apache.org/commons/dbcp/api/org/apache/commons/dbcp/BasicDataSource.html
>>>>>>
>>>>>>     ds.setMaxActive(10);
>>>>>>     ds.setMaxIdle(5);
>>>>>>     ds.setMaxWait(10000);
>>>>>>
>>>>>>     return ds;
>>>>>>   }
>>>>>>
>>>>>> Does that still work?
>>>>> Hmmm, I was assuming that BasicDataSource didn't actually do any
>>>>> pooling itself, and that you needed another layer on top to manage a
>>>>> connection pool -- that seems to be how all previous revisions of
>>>>> JDBCConnectionPool worked, so I guess I wasn't alone in thinking
>>>>> this.  But yes, BasicDataSource does seem to do pooling itself
>>>>> (confirmed by reading the source), so maybe your simpler version is
>>>>> a better idea.  It certainly works okay for me.
>>>>>
>>>>>            Thomas.
>>>> That's what I thought should have happened :). Can I suggest that
>>>> this revised version goes into CVS? Anyone got any objections?
>>>>
>>>> Andy
>>>> _______________________________________________
>>>> biojava-dev mailing list
>>>> biojava-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>>

> ------------------------------------------------------------------------

> /*
>  *                    BioJava development code
>  *
>  * This code may be freely distributed and modified under the
>  * terms of the GNU Lesser General Public Licence.  This should
>  * be distributed with the code.  If you do not have a copy,
>  * see:
>  *
>  *      http://www.gnu.org/copyleft/lesser.html
>  *
>  * Copyright for this code is held jointly by the individual
>  * authors.  These should be listed in @author doc comments.
>  *
>  * For more information on the BioJava project and its aims,
>  * or to join the biojava-l mailing list, visit the home page
>  * at:
>  *
>  *      http://www.biojava.org/
>  *
>  */
> package org.biojava.utils;

> import javax.sql.DataSource;

> import org.apache.commons.dbcp.BasicDataSource;
> import org.apache.commons.dbcp.PoolingDataSource;
> import org.apache.commons.pool.ObjectPool;

> /**
> * Returns a DataSource that implements connection pooling
> *
> * Uses Jakarta Commons DBCP and Pool packages.
> * See the description of the dbcp package at 
> * http://jakarta.apache.org/commons/dbcp/api/overview-summary.html#overview_description
> *
> * @author Simon Foote
> * @author Len Trigg
> */

> public class JDBCPooledDataSource {

>   public static DataSource getDataSource(final String driver, 
>                                          final String url,
>                                          final String user,
>                                          final String pass)
>     throws Exception {

>     BasicDataSource ds = new BasicDataSource();
>     ds.setUrl(url);
>     ds.setDriverClassName(driver);
>     ds.setUsername(user);
>     ds.setPassword(pass);
>     // Set BasicDataSource properties such as maxActive and maxIdle, as described in
>     // http://jakarta.apache.org/commons/dbcp/api/org/apache/commons/dbcp/BasicDataSource.html
>     ds.setMaxActive(10);
>     ds.setMaxIdle(5);
>     ds.setMaxWait(10000);

>     return dataSource;
>   }


>   // Adds simple equals and hashcode methods so that we can compare if
>   // two connections are to the same database. This will fail if the
>   // DataSource is redirected to another database etc (I doubt this is
>   // ever likely to be used).
>   /**
>    * @depercated This is no longer used in favor of {@link BasicDataSource}
>    * from DBCP
>    */
>   static class MyPoolingDataSource extends PoolingDataSource {
>     final String source;
>     public MyPoolingDataSource(ObjectPool connectionPool, String source) {
>       super(connectionPool);
>       this.source = source;
>     }
>     public boolean equals(Object o2) {
>       if ((o2 == null) || !(o2 instanceof MyPoolingDataSource)) {
>         return false;
>       }
>       MyPoolingDataSource b2 = (MyPoolingDataSource) o2;
>       return source.equals(b2.source);
>     }
>     public int hashCode() {
>       return source.hashCode();
>     }
>   }


>   public static void main(String[] args) {
>     try {
>       DataSource ds1 = getDataSource("org.hsqldb.jdbcDriver", "jdbc:hsqldb:/tmp/hsqldb/biosql", "sa", "");
>       DataSource ds2 = getDataSource("org.hsqldb.jdbcDriver", "jdbc:hsqldb:/tmp/hsqldb/biosql", "sa", "");
>       System.err.println(ds1);
>       System.err.println(ds2);
>       System.err.println(ds1.equals(ds2));
>     } catch (Exception e) {
>       e.printStackTrace();
>     }
>   }
> }
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From ayates at ebi.ac.uk  Wed Jan 31 13:25:12 2007
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 31 Jan 2007 13:25:12 +0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <45C094AE.1030101@ebi.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>	<45C0781B.7030304@ebi.ac.uk>	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>	<45C08639.7080600@ebi.ac.uk>	<8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>
	<45C08B7A.3060102@ebi.ac.uk> <45C08E4E.2050308@ebi.ac.uk>
	<45C090A6.10909@ebi.ac.uk> <45C094AE.1030101@ebi.ac.uk>
Message-ID: <45C098B8.7030107@ebi.ac.uk>

Cheers mate. If this hash/equals is a problem then this can be solved 
later on.

Richard Holland wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> I've committed your changes Andy.
> 
> Thomas, I wouldn't worry about OntologySQL. It's highly deprecated and
> not supported - the whole biojavax/Hibernate thing made that code redundant.
> 
> Richard.
> 
> Andy Yates wrote:
>> Okay I've attached the fix here.
>>
>> I just did this in a text editor but I believe that the imports are
>> okay. If you can just do a quick scan as well to make sure I haven't
>> deleted anything that was very important.
>>
>> I'll get on to the helpdesk now as well :)
>>
>> Andy
>>
>> Richard Holland wrote:
>> Andy could you make the change to your local copy of the source file and
>> email the file to me, that way I can make sure I don't get it wrong when
>> I commit it.
>>
>> Richard.
>>
>> PS. You should probably have your own CVS account - email the OBF
>> helpdesk and ask for one, saying I told you to. :)
>>
>>
>> Andy Yates wrote:
>>>>> Thomas Down wrote:
>>>>>> On 31 Jan 2007, at 12:06, Andy Yates wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> Sorry I was meaning if that if that method just becomes:
>>>>>>>
>>>>>>> public static DataSource getDataSource(final String driver,
>>>>>>>                                          final String url,
>>>>>>>                                          final String user,
>>>>>>>                                          final String pass)
>>>>>>>     throws Exception {
>>>>>>>
>>>>>>>     BasicDataSource ds = new BasicDataSource();
>>>>>>>     ds.setUrl(url);
>>>>>>>     ds.setDriverClassName(driver);
>>>>>>>     ds.setUsername(user);
>>>>>>>     ds.setPassword(pass);
>>>>>>>     // Set BasicDataSource properties such as maxActive and
>>>>>>> maxIdle, as described in
>>>>>>>     //
>>>>>>> http://jakarta.apache.org/commons/dbcp/api/org/apache/commons/dbcp/BasicDataSource.html
>>>>>>>
>>>>>>>     ds.setMaxActive(10);
>>>>>>>     ds.setMaxIdle(5);
>>>>>>>     ds.setMaxWait(10000);
>>>>>>>
>>>>>>>     return ds;
>>>>>>>   }
>>>>>>>
>>>>>>> Does that still work?
>>>>>> Hmmm, I was assuming that BasicDataSource didn't actually do any
>>>>>> pooling itself, and that you needed another layer on top to manage a
>>>>>> connection pool -- that seems to be how all previous revisions of
>>>>>> JDBCConnectionPool worked, so I guess I wasn't alone in thinking
>>>>>> this.  But yes, BasicDataSource does seem to do pooling itself
>>>>>> (confirmed by reading the source), so maybe your simpler version is
>>>>>> a better idea.  It certainly works okay for me.
>>>>>>
>>>>>>            Thomas.
>>>>> That's what I thought should have happened :). Can I suggest that
>>>>> this revised version goes into CVS? Anyone got any objections?
>>>>>
>>>>> Andy
>>>>> _______________________________________________
>>>>> biojava-dev mailing list
>>>>> biojava-dev at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>>>
> 
>> ------------------------------------------------------------------------
> 
>> /*
>>  *                    BioJava development code
>>  *
>>  * This code may be freely distributed and modified under the
>>  * terms of the GNU Lesser General Public Licence.  This should
>>  * be distributed with the code.  If you do not have a copy,
>>  * see:
>>  *
>>  *      http://www.gnu.org/copyleft/lesser.html
>>  *
>>  * Copyright for this code is held jointly by the individual
>>  * authors.  These should be listed in @author doc comments.
>>  *
>>  * For more information on the BioJava project and its aims,
>>  * or to join the biojava-l mailing list, visit the home page
>>  * at:
>>  *
>>  *      http://www.biojava.org/
>>  *
>>  */
>> package org.biojava.utils;
> 
>> import javax.sql.DataSource;
> 
>> import org.apache.commons.dbcp.BasicDataSource;
>> import org.apache.commons.dbcp.PoolingDataSource;
>> import org.apache.commons.pool.ObjectPool;
> 
>> /**
>> * Returns a DataSource that implements connection pooling
>> *
>> * Uses Jakarta Commons DBCP and Pool packages.
>> * See the description of the dbcp package at 
>> * http://jakarta.apache.org/commons/dbcp/api/overview-summary.html#overview_description
>> *
>> * @author Simon Foote
>> * @author Len Trigg
>> */
> 
>> public class JDBCPooledDataSource {
> 
>>   public static DataSource getDataSource(final String driver, 
>>                                          final String url,
>>                                          final String user,
>>                                          final String pass)
>>     throws Exception {
> 
>>     BasicDataSource ds = new BasicDataSource();
>>     ds.setUrl(url);
>>     ds.setDriverClassName(driver);
>>     ds.setUsername(user);
>>     ds.setPassword(pass);
>>     // Set BasicDataSource properties such as maxActive and maxIdle, as described in
>>     // http://jakarta.apache.org/commons/dbcp/api/org/apache/commons/dbcp/BasicDataSource.html
>>     ds.setMaxActive(10);
>>     ds.setMaxIdle(5);
>>     ds.setMaxWait(10000);
> 
>>     return dataSource;
>>   }
> 
> 
>>   // Adds simple equals and hashcode methods so that we can compare if
>>   // two connections are to the same database. This will fail if the
>>   // DataSource is redirected to another database etc (I doubt this is
>>   // ever likely to be used).
>>   /**
>>    * @depercated This is no longer used in favor of {@link BasicDataSource}
>>    * from DBCP
>>    */
>>   static class MyPoolingDataSource extends PoolingDataSource {
>>     final String source;
>>     public MyPoolingDataSource(ObjectPool connectionPool, String source) {
>>       super(connectionPool);
>>       this.source = source;
>>     }
>>     public boolean equals(Object o2) {
>>       if ((o2 == null) || !(o2 instanceof MyPoolingDataSource)) {
>>         return false;
>>       }
>>       MyPoolingDataSource b2 = (MyPoolingDataSource) o2;
>>       return source.equals(b2.source);
>>     }
>>     public int hashCode() {
>>       return source.hashCode();
>>     }
>>   }
> 
> 
>>   public static void main(String[] args) {
>>     try {
>>       DataSource ds1 = getDataSource("org.hsqldb.jdbcDriver", "jdbc:hsqldb:/tmp/hsqldb/biosql", "sa", "");
>>       DataSource ds2 = getDataSource("org.hsqldb.jdbcDriver", "jdbc:hsqldb:/tmp/hsqldb/biosql", "sa", "");
>>       System.err.println(ds1);
>>       System.err.println(ds2);
>>       System.err.println(ds1.equals(ds2));
>>     } catch (Exception e) {
>>       e.printStackTrace();
>>     }
>>   }
>> }
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From jburdick at keyfitz.org  Mon Jan 22 16:46:44 2007
From: jburdick at keyfitz.org (Josh Burdick)
Date: Mon, 22 Jan 2007 16:46:44 -0000
Subject: [Biojava-dev] reading a subsequence from a .nib file
Message-ID: <1169483375.5340.39.camel@localhost.localdomain>

  I wrote some code to read a chunk of DNA sequence from a file in Jim
Kent's blat ".nib" file format.  This is a simple format using four
bits/base.

  I didn't attach the code, to avoid spamming the whole list; but it,
and a (very crude!) JUnit test, are at

http://www.keyfitz.org/jburdick/read_nib_file_java/NibFile.java
http://www.keyfitz.org/jburdick/read_nib_file_java/NibFileTest.java

  You could use 2 bits/base, but then you can't have ambiguous bases.  4
bits/base seems like a reasonable compromise; plus sites that have
"blat" installed will need to have the .nib files on a server somewhere
anyway, and this way repeat-masking can be included, which may be
convenient.

  Also, it doesn't support writing a .nib file; again, presumably people
will be using Jim Kent's faToNib program to do that.

  It would need some tweaking to be included in BioJava, because it
returns a plain String of ACGT, instead of a PackedSequence object.
(Probably this would just involve rewriting the setupBuffer() and
addToBuffer() methods in the code.)  Also, the coordinate information
could come from a Range object.

  If similar code is already somewhere in BioJava, please ignore this;
but I couldn't find it with thirty seconds of Googling, so I figured it
hadn't been written...

Josh Burdick
programmer, Vivian Cheung's lab, Children's Hospital of Philadelphia
jburdick at keyfitz.org




From ayates at ebi.ac.uk  Wed Jan 31 12:50:53 2007
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 31 Jan 2007 12:50:53 -0000
Subject: [Biojava-dev] JDBCPooledDataSource regression
In-Reply-To: <45C08E4E.2050308@ebi.ac.uk>
References: <416B41DF-91E1-4D1F-A4B4-799FE712B032@sanger.ac.uk>	<45C0781B.7030304@ebi.ac.uk>	<5DDBC6F5-7DC3-4446-A982-3CD9B3931A06@sanger.ac.uk>	<45C08639.7080600@ebi.ac.uk>	<8689C307-0643-46D9-90A6-A9958681D1D0@sanger.ac.uk>
	<45C08B7A.3060102@ebi.ac.uk> <45C08E4E.2050308@ebi.ac.uk>
Message-ID: <45C090A6.10909@ebi.ac.uk>

Okay I've attached the fix here.

I just did this in a text editor but I believe that the imports are 
okay. If you can just do a quick scan as well to make sure I haven't 
deleted anything that was very important.

I'll get on to the helpdesk now as well :)

Andy

Richard Holland wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> Andy could you make the change to your local copy of the source file and
> email the file to me, that way I can make sure I don't get it wrong when
> I commit it.
> 
> Richard.
> 
> PS. You should probably have your own CVS account - email the OBF
> helpdesk and ask for one, saying I told you to. :)
> 
> 
> Andy Yates wrote:
>> Thomas Down wrote:
>>> On 31 Jan 2007, at 12:06, Andy Yates wrote:
>>>
>>>> Hi,
>>>>
>>>> Sorry I was meaning if that if that method just becomes:
>>>>
>>>> public static DataSource getDataSource(final String driver,
>>>>                                          final String url,
>>>>                                          final String user,
>>>>                                          final String pass)
>>>>     throws Exception {
>>>>
>>>>     BasicDataSource ds = new BasicDataSource();
>>>>     ds.setUrl(url);
>>>>     ds.setDriverClassName(driver);
>>>>     ds.setUsername(user);
>>>>     ds.setPassword(pass);
>>>>     // Set BasicDataSource properties such as maxActive and maxIdle, 
>>>> as described in
>>>>     // 
>>>> http://jakarta.apache.org/commons/dbcp/api/org/apache/commons/dbcp/BasicDataSource.html 
>>>>
>>>>     ds.setMaxActive(10);
>>>>     ds.setMaxIdle(5);
>>>>     ds.setMaxWait(10000);
>>>>
>>>>     return ds;
>>>>   }
>>>>
>>>> Does that still work?
>>> Hmmm, I was assuming that BasicDataSource didn't actually do any pooling 
>>> itself, and that you needed another layer on top to manage a connection 
>>> pool -- that seems to be how all previous revisions of 
>>> JDBCConnectionPool worked, so I guess I wasn't alone in thinking this.  
>>> But yes, BasicDataSource does seem to do pooling itself (confirmed by 
>>> reading the source), so maybe your simpler version is a better idea.  It 
>>> certainly works okay for me.
>>>
>>>            Thomas.
>> That's what I thought should have happened :). Can I suggest that this 
>> revised version goes into CVS? Anyone got any objections?
>>
>> Andy
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
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