[Biojava-l] RE: Sequence serialization exception
- AlphabetManagerproblem?
Vasa Curcin
vc100 at doc.ic.ac.uk
Tue Oct 21 23:30:47 EDT 2003
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)
>
>
>
>
>
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>
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