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:[EMAIL PROTECTED]
Sent: Wed 1/10/2003 1:25 a.m.
To: Schreiber, Mark; [EMAIL PROTECTED]
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:[EMAIL PROTECTED]
Sent: Tuesday, September 30, 2003 6:28 AM
To: [EMAIL PROTECTED]; [EMAIL PROTECTED]
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:[EMAIL PROTECTED]
Sent: Tue 30/09/2003 10:45 a.m.
To: [EMAIL PROTECTED]
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:[EMAIL PROTECTED]
Sent: Monday, September 29, 2003 2:01 PM
Cc: '[EMAIL PROTECTED]'
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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