[Biojava-dev] RE: [Biojava-l] RE: Sequence serialization exception
- AlphabetManagerproblem?
Schreiber, Mark
mark.schreiber at agresearch.co.nz
Thu Oct 23 16:45:24 EDT 2003
Hi Vasa -
The problem is that Biojava requires it's Symbol instances to be Flywieght (basically Singletons). This means that the Met symbol == the Met Symbol. Ie there is only one of them. In most cases the way this is done is that the Symbols name is serialized not the Symbol. If the Symbol where serialized it would be duplicated on the receiving JVM and the == operation would no longer return true which would be a disaster.
It actually works for almost everything except protein Symbols as they are members of two Alphabets PROTEIN and PROTEIN-TERM. The PROTEIN-TERM alphabet contains the * symbol which is used to represent the translation of a stop codon for representation of complete frame translations.
The problem is in the class WellKnownAtomicSymbol. This is a private inner class of AlphabetManager. It has a readResolve method called during Serialization which replaces the WellKnownAtomicSymbol on the ObjectOutputStream with a place holder object called OPH (a private inner class of WellKnownAtomicSymbol) which holds the name of the Symbol. When the OPH is de serialized it's readResolve() method is called which calls the AlphabetManager method symbolForName(name). This goes and looks up a HashMap of names to Symbols. For some reason when the AlphabetManger initializes it is not putting the names of the protein Symbols into the HashMap.
That is actually the root cause of the problem and not the Serialzation itself. I will desperately try to look at this over the weekend and fix it. If someone else gets to it first that's cool too.
- Mark
-----Original Message-----
From: Vasa Curcin [mailto:vc100 at doc.ic.ac.uk]
Sent: Thursday, 23 October 2003 9:48 p.m.
To: Schreiber, Mark
Subject: Re: [Biojava-l] RE: Sequence serialization exception - AlphabetManagerproblem?
Hi,
Could you possibly tell me how Biojava serializes protein sequences. I
need this functionality pretty badly, so I will most likely try to hack it.
Regards,
Vasa
Schreiber, Mark wrote:
>Hi -
>
>Binary serialization of protein sequences is currently broken. I need
>to move to a pattern of using LSIDs to identify them uniquely. This
>should fix the problem. Just need to find time to do it <sigh>
>
>- Mark
>
>
>-----Original Message-----
>From: Vasa Curcin [mailto:vc100 at doc.ic.ac.uk]
>Sent: Wednesday, 22 October 2003 4:31 p.m.
>To: Schreiber, Mark
>Cc: msouthern at exsar.com; biojava-l at biojava.org
>Subject: Re: [Biojava-l] RE: Sequence serialization exception - AlphabetManagerproblem?
>
>
>Having exactly the same problem here with serializing SimpleSequence
>objects containing proteins. It doesn't like MET... Was there a solution
>found?
>
>Vasa
>
>Schreiber, Mark wrote:
>
>
>
>>Hi -
>>
>>I am not getting the exception you have below (which looks like one
>>
>>
>>from before we fixed the EmblFileFormer). I am however getting an
>>InvalidObjectException which is comming from something odd in the AlphabetManager. I'll have a look into it.
>
>
>>java.io.InvalidObjectException: Couldn't resolve symbol:MET at
>>org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol$OPH.readResolve(AlphabetManager.java:1480)
>>
>>- Mark
>>
>>
>> -----Original Message-----
>> From: Mark Southern [mailto:msouthern at exsar.com]
>> Sent: Tue 7/10/2003 3:50 a.m.
>> To: Schreiber, Mark; biojava-l at biojava.org
>> Cc:
>> Subject: RE: [Biojava-l] RE: Sequence serialization exception -
>>AlphabetManagerproblem?
>>
>>
>>
>> Hi Mark,
>>
>> I have downloaded and tested the latest EmblFileFormer.java (1.24.2.1) and
>> it can now successfully write out a swissprot format file after first having
>> written it in (Thank you).
>> However, i am still seeing an exception attempting to read in a serialized
>> sequence. Test code and exception below.
>>
>> Best regards,
>>
>> Mark.
>>
>> //------------------------------------------
>>
>> public static void main(String[] args) throws Exception{
>> File file = new File("c:\\temp\\sequence.ser");
>> String seqFile = "c:\\temp\\KAP0_BOVIN.swiss";
>>
>> SequenceIterator iter = (SequenceIterator) SeqIOTools.fileToBiojava(
>> SeqIOConstants.SWISSPROT, new BufferedReader( new FileReader( seqFile
>>) ) );
>>
>> Sequence seq = iter.nextSequence();
>>
>> // this now works
>> //SeqIOTools.biojavaToFile( SeqIOConstants.SWISSPROT, System.out,
>> seq );
>>
>> ObjectOutputStream out = new ObjectOutputStream( new
>> FileOutputStream(file) );
>> out.writeObject( seq );
>> out.flush();
>> out.close();
>>
>> ObjectInputStream in = new ObjectInputStream( new
>> FileInputStream(file) );
>> // still get an error deserializing
>> seq = (Sequence) in.readObject();
>> in.close();
>> }
>>
>> //------------------------------------------
>> org.biojava.bio.symbol.IllegalSymbolException: Symbol ALA not found in
>> alphabet DNA
>> at
>> org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:278)
>> at
>> org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.val
>> idate(AlphabetManager.java:1423)
>> at
>> org.biojava.bio.seq.io.CharacterTokenization._tokenizeSymbol(CharacterTokeni
>> zation.java:178)
>> at
>> org.biojava.bio.seq.io.CharacterTokenization.tokenizeSymbol(CharacterTokeniz
>> ation.java:191)
>> at
>> org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.tokenize
>> Symbol(AlphabetManager.java:1276)
>> at
>> org.biojava.bio.seq.io.AbstractGenEmblFileFormer.formatTokenBlock(AbstractGe
>> nEmblFileFormer.java:337)
>> at
>> org.biojava.bio.seq.io.EmblFileFormer.addSymbols(EmblFileFormer.java:211)
>> rethrown as org.biojava.bio.symbol.IllegalAlphabetException: DNA not
>> tokenizing
>> at
>> org.biojava.bio.seq.io.EmblFileFormer.addSymbols(EmblFileFormer.java:224)
>> at
>> org.biojava.bio.seq.io.SeqIOEventEmitter.getSeqIOEvents(SeqIOEventEmitter.ja
>> va:125)
>> rethrown as org.biojava.bio.BioError: An internal error occurred processing
>> symbols
>> at
>> org.biojava.bio.seq.io.SeqIOEventEmitter.getSeqIOEvents(SeqIOEventEmitter.ja
>> va:137)
>> at
>> org.biojava.bio.seq.io.EmblLikeFormat.writeSequence(EmblLikeFormat.java:289)
>> at
>> org.biojava.bio.seq.io.EmblLikeFormat.writeSequence(EmblLikeFormat.java:253)
>> at
>> org.biojava.bio.seq.io.SeqIOTools.writeSwissprot(SeqIOTools.java:316)
>> at org.biojava.bio.seq.io.SeqIOTools.seqToFile(SeqIOTools.java:1078)
>> at
>> org.biojava.bio.seq.io.SeqIOTools.biojavaToFile(SeqIOTools.java:870)
>> at com.exsar.test.SerializeTest.main(SerializeTest.java:36)
>>
>>
>> -----Original Message-----
>> From: Schreiber, Mark [mailto:mark.schreiber at agresearch.co.nz]
>> Sent: Wednesday, October 01, 2003 1:54 AM
>> To: msouthern at exsar.com; biojava-l at biojava.org
>> Subject: RE: [Biojava-l] RE: Sequence serialization exception -
>> AlphabetManagerproblem?
>>
>>
>> OK -
>>
>> I tracked it down to a bug in the EMBLFileFormer (which gets coopted for
>> SwissProt writing). It assumed a DNA alphabet and therefore couldn't write
>> protein in SwissProt format.
>>
>> I have checked it into CVS, I will port it back to the 1.3 branch of CVS
>> shortly.
>>
>> - Mark
>> -----Original Message-----
>> From: Mark Southern [mailto:msouthern at exsar.com]
>> Sent: Wed 1/10/2003 1:25 a.m.
>> To: Schreiber, Mark; biojava-l at biojava.org
>> Cc:
>> Subject: RE: [Biojava-l] RE: Sequence serialization exception -
>> AlphabetManagerproblem?
>>
>>
>> Hi Mark,
>>
>> I did also have an error with binary serialization. I was just trying to
>> approach to problem from a different direction. B/c that also was a problem
>> with finding / determining a protein symbol, i wondered if was coming from
>> AlphabetManager rather than the Swissprot writing. I include below the code
>> fragment along with the serialization error.
>>
>> Best regards,
>>
>> Mark.
>>
>>
>> public static void main(String[] args) throws Exception{
>> File file = new File("c:\\temp\\sequence.ser");
>> String seqFile = "c:\\temp\\KAP0_BOVIN.swiss";
>>
>> SequenceIterator iter = (SequenceIterator) SeqIOTools.fileToBiojava(
>> SeqIOConstants.SWISSPROT
>> ,
>> new BufferedReader( new FileReader( seqFile ) ) );
>>
>> Sequence seq = iter.nextSequence();
>>
>> System.out.println("\nWriting Sequence object");
>> ObjectOutputStream out = new ObjectOutputStream( new
>> FileOutputStream(file) );
>> out.writeObject( seq );
>> out.flush();
>> out.close();
>>
>> System.out.println("\nReading Sequence object");
>> ObjectInputStream in = new ObjectInputStream( new
>> FileInputStream(file) );
>> seq = (Sequence) in.readObject();
>> in.close();
>>
>> }
>>
>> Writing Sequence object
>> Reading Sequence object
>> java.io.InvalidObjectException: Couldn't resolve symbol:ALA
>> at
>> org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol$OPH.readResolve
>> (AlphabetManager.java:1480)
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39
>> )
>> at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl
>> .java:25)
>> at java.lang.reflect.Method.invoke(Method.java:324)
>> at
>> java.io.ObjectStreamClass.invokeReadResolve(ObjectStreamClass.java:911)
>> at
>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1655)
>> at
>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274)
>> at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1603)
>> at
>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1271)
>> at
>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845)
>> at
>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769)
>> at
>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646)
>> at
>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274)
>> at
>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845)
>> at
>> java.io.ObjectInputStream.defaultReadObject(ObjectInputStream.java:452)
>> at
>> org.biojava.bio.seq.impl.SimpleSequence.readObject(SimpleSequence.java:119)
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39
>> )
>> at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl
>> .java:25)
>> at java.lang.reflect.Method.invoke(Method.java:324)
>> at
>> java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824)
>> at
>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746)
>> at
>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646)
>> at
>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274)
>> at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324)
>> at com.exsar.test.SerializeTest.main(SerializeTest.java:38)
>> Exception in thread "main"
>>
>>
>>
>> -----Original Message-----
>> From: Schreiber, Mark [mailto:mark.schreiber at agresearch.co.nz]
>> Sent: Tuesday, September 30, 2003 6:28 AM
>> To: msouthern at exsar.com; biojava-l at biojava.org
>> Subject: RE: [Biojava-l] RE: Sequence serialization exception -
>> AlphabetManagerproblem?
>>
>>
>> Hi -
>>
>> I was a bit thrown off at first cause I thought you meant there was an error
>> in binary serialization. There seems to be a problem with SwissProt writing.
>> I've commited an addition to SeqIOToolsTest in biojava live that replicates
>> the error but I haven't got time to track it down just yet. If some one else
>> doesn't get it I'll probably find it tommorrow.
>>
>> - Mark
>>
>> -----Original Message-----
>> From: Mark Southern [mailto:msouthern at exsar.com]
>> Sent: Tue 30/09/2003 10:45 a.m.
>> To: biojava-l at biojava.org
>> Cc:
>> Subject: [Biojava-l] RE: Sequence serialization exception -
>> AlphabetManagerproblem?
>>
>>
>> Appologies for following up on my own post. What follows is a simpler test
>> than the serialization I attempted before.
>>
>> Consider the bit of code below and corresponding error message;
>>
>> For some reason, the protein sequence is being treated as a dna sequence. Is
>> there something I am missing with respect to how AlphabetManager treats dna
>> and protein alphabets?
>>
>> Any explainations would be most welcome.
>>
>> Thanks again,
>>
>> Mark.
>>
>>
>>
>>//--------------------------------------------------------------------
>>----
>>
>> public static void main(String[] args) throws Exception{
>> String seqFile = "c:\\temp\\KAP0_BOVIN.swiss";
>> SequenceIterator iter = (SequenceIterator)
>> SeqIOTools.fileToBiojava(SeqIOConstants.SWISSPROT
>>
>> ,new BufferedReader( new FileReader( seqFile ) ) );
>> Sequence seq = iter.nextSequence();
>> SeqIOTools.biojavaToFile( SeqIOConstants.SWISSPROT, System.out,
>> seq );
>> }
>>
>>
>> org.biojava.bio.symbol.IllegalSymbolException: Symbol ALA not found in
>> alphabet DNA
>> at
>> org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:278)
>> at
>> org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.val
>> idate(AlphabetManager.java:1423)
>> at
>> org.biojava.bio.seq.io.CharacterTokenization._tokenizeSymbol(CharacterTokeni
>> zation.java:178)
>> at
>> org.biojava.bio.seq.io.CharacterTokenization.tokenizeSymbol(CharacterTokeniz
>> ation.java:191)
>> at
>> org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.tokenize
>> Symbol(AlphabetManager.java:1276)
>> at
>> org.biojava.bio.seq.io.AbstractGenEmblFileFormer.formatTokenBlock(AbstractGe
>> nEmblFileFormer.java:337)
>> at
>> org.biojava.bio.seq.io.EmblFileFormer.addSymbols(EmblFileFormer.java:211)
>> rethrown as org.biojava.bio.symbol.IllegalAlphabetException: DNA not
>> tokenizing
>> at
>> org.biojava.bio.seq.io.EmblFileFormer.addSymbols(EmblFileFormer.java:224)
>> at
>> org.biojava.bio.seq.io.SeqIOEventEmitter.getSeqIOEvents(SeqIOEventEmitter.ja
>> va:125)
>> rethrown as org.biojava.bio.BioError: An internal error occurred processing
>> symbols
>> at
>> org.biojava.bio.seq.io.SeqIOEventEmitter.getSeqIOEvents(SeqIOEventEmitter.ja
>> va:137)
>> at
>> org.biojava.bio.seq.io.EmblLikeFormat.writeSequence(EmblLikeFormat.java:289)
>> at
>> org.biojava.bio.seq.io.EmblLikeFormat.writeSequence(EmblLikeFormat.java:253)
>> at
>> org.biojava.bio.seq.io.SeqIOTools.writeSwissprot(SeqIOTools.java:316)
>> at org.biojava.bio.seq.io.SeqIOTools.seqToFile(SeqIOTools.java:1078)
>> at
>> org.biojava.bio.seq.io.SeqIOTools.biojavaToFile(SeqIOTools.java:870)
>> at com.exsar.test.SerializeTest.main(SerializeTest.java:24)
>>
>>
>>
>> -----Original Message-----
>> From: Mark Southern [mailto:msouthern at exsar.com]
>> Sent: Monday, September 29, 2003 2:01 PM
>> Cc: 'biojava-l at biojava.org'
>> Subject: Sequence serialization exception
>>
>>
>> I am getting the following exception when trying to serialize a protein
>> sequence. I am using biojava 1.3. Can anyone please explain to me
>>why?
>>
>> Many thanks,
>>
>> Mark.
>>
>>
>> java.io.InvalidObjectException: Couldn't resolve symbol:SER
>> at
>> org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol$OPH.readResolve
>> (AlphabetManager.java:1441)
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39
>> )
>> at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl
>> .java:25)
>> at java.lang.reflect.Method.invoke(Method.java:324)
>> at
>> java.io.ObjectStreamClass.invokeReadResolve(ObjectStreamClass.java:911)
>> at
>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1655)
>> at
>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274)
>> at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1603)
>> at
>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1271)
>> at
>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845)
>> at
>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769)
>> at
>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646)
>> at
>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274)
>> at
>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845)
>> at
>> java.io.ObjectInputStream.defaultReadObject(ObjectInputStream.java:452)
>> at
>> org.biojava.bio.seq.impl.SimpleSequence.readObject(SimpleSequence.java:119)
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39
>> )
>> at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl
>> .java:25)
>> at java.lang.reflect.Method.invoke(Method.java:324)
>> at
>> java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824)
>> at
>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746)
>> at
>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646)
>> at
>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274)
>> at
>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845)
>> at
>> java.io.ObjectInputStream.defaultReadObject(ObjectInputStream.java:452)
>> at org.biojava.bio.seq.ViewSequence.readObject(ViewSequence.java:93)
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39
>> )
>> at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl
>> .java:25)
>> at java.lang.reflect.Method.invoke(Method.java:324)
>> at
>> java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824)
>> at
>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746)
>> at
>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646)
>> at
>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274)
>> at
>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845)
>> at
>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769)
>> at
>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646)
>> at
>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274)
>> at
>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845)
>> at
>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769)
>> at
>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646)
>> at
>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274)
>> at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324)
>> at java.util.HashMap.readObject(HashMap.java:985)
>> at sun.reflect.GeneratedMethodAccessor6.invoke(Unknown Source)
>> at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl
>> .java:25)
>> at java.lang.reflect.Method.invoke(Method.java:324)
>> at
>> java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824)
>> at
>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746)
>> at
>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646)
>> at
>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274)
>> at
>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845)
>> at
>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769)
>> at
>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646)
>> at
>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274)
>> at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324)
>> at java.util.HashMap.readObject(HashMap.java:986)
>> at sun.reflect.GeneratedMethodAccessor6.invoke(Unknown Source)
>> at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl
>> .java:25)
>> at java.lang.reflect.Method.invoke(Method.java:324)
>> at
>> java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:824)
>> at
>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1746)
>> at
>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646)
>> at
>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274)
>> at
>> java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1845)
>> at
>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1769)
>> at
>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1646)
>> at
>> java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1274)
>> at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324)
>> at com.exsar.hdex.model.calc.Test.main(Test.java:104)
>>
>>
>>
>>
>>
>> _______________________________________________
>> Biojava-l mailing list - Biojava-l at biojava.org
>> http://biojava.org/mailman/listinfo/biojava-l
>>
>>
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