[Biojava-l] problem running demos from the biojava-live dir ...

[Matthew Pocock]

Hi. My development biojava copy is in C:\stuff\biojava\biojava-live on 
my PC. I can find Alphabetmanager.xml here:

C:\stuff\biojava\biojava-live\resources\org\biojava\bio\symbol>ls
AlphabetManager.xml  AlphabetManager.xml~  CVS

To check if the resource is in the jar I type something like this:

C:\stuff\biojava\biojava-live\ant-build>jar -tf biojava.jar > out

C:\stuff\biojava\biojava-live\ant-build>grep AlphabetManager.xml out
org/biojava/bio/symbol/AlphabetManager.xml

To check the version of Java, I typed:

C:\>java -version
java version "1.4.0-beta"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.0-beta-b65)
Java HotSpot(TM) Client VM (build 1.4.0-beta-b65, mixed mode)

What kind of output do you get when you do similar things?

Matthew

sarathchandra wrote:

> hi pocock
>   I have tried to check the existence of the file
> alphabetmanager.xml in the directory tools nested
> inside resources i think this file  should be
> somewhere like this
> resources/../../tools/alphabetmanager.xml but the file
> alphabetmanager.xml isnt present in the tools
> directory.. is this some where the problem is arising
> ... if this is so adding resources deliberately to my
> classpath wouldnt help i guess, but still i will check
> it.however do u feel it is the problem with the
> biojava.jar file? may be? or may be not? have you ever
> faced such problems like the program getting compiled
> well but still the unhealthy exceptions like the one i
> get.
> awaiting your help
> from sarath
> --- Matthew Pocock <mrp@sanger.ac.uk> wrote:
> 
>>Hi Sarath,
>>
>>Weird. It sounds like alphabetmanager.xml can't be
>>found within the 
>>biojava.jar repository. To test this out, can you
>>add the 'resources' 
>>directory to the beginning of your classpath
>>explicitly? If the program 
>>works then Java is having trouble finding the file
>>within the jar file. 
>>Could you check that alphabetmanager.xml is in the
>>same directory as 
>>AlphabetManager.class in the jar?
>>
>>I've occasionaly come up against strange resource
>>resolution problems 
>>(do you or don't you add a leading slash to the
>>path-name?). Mabey it is 
>>one of these.
>>
>>Matthew
>>
>>ps I've never seen a stack-trace quite like this.
>>What Java are you running?
>>
>>
>>sarathchandra wrote:
>>
>>
>>>hi thomas and pocock
>>>   I have been using biojava for quite some time
>>>now,But recently i installed red hat linux 7.1 and
>>>added biojava.jar , xerces.jar,
>>>
>>xml.jar,bytecode.jar
>>
>>>and the jakarta-regexp.jar but inspite of this
>>>
>>when i
>>
>>>try to run the demos from the biojava-live
>>>
>>directory i
>>
>>>am getting the followingstack trace for the
>>>
>>programs
>>
>>>[sarath@localhost demos]javac seq/GCCgbk.java
>>>[sarath@localhost demos]java  seq.GCCgbk
>>>
>>seq/utrs.fa
>>
>>> java.lang.ExceptionInIntializerError: [exception
>>>
>>was
>>
>>>org.biojava.bio.bioerror: unable to initialize
>>>AlphabetManager]
>>>java.lang.NullpointerException
>>> rethrown as org.biojava.bio.BioError:unable to
>>>initialize AlphabetManager
>>> at
>>>
>>>
> java.lang.Throwable.FillInstanceTrace(Throwable.java:native)
> 
>>>at java.lang.Throwable.<init>(Throwable.java:38)
>>>at java.lang.Error.<init>(Error.java:21)
>>>at org.biojava.utils.NestedError.<init>(Nested
>>>Error.java:60)
>>>at
>>>
>>org.biojava.bio.bioError,<init>(BioError.java:48)
>>
>>>     Hope this stack trace will help you to tell
>>>
>>me
>>
>>>whats wrong with the running of programs is it
>>>
>>because
>>
>>>the file alphabetmanager.xml in manifest directory
>>>
>>is
>>
>>>missing as i found that such file exists in this
>>>directory.. Anyway hope to hear an early reply
>>>
>>from
>>
>>>you
>>>from sarath
>>>
>>>
>>>
>>>=====
>>>
> 
> 
> =====
> TIME AND TIDE WAIT FOR NO MAN
> KNOWLEDGE IS POWER
> 
> sarath chandra J
> B.tech 3rd yr
> IIT Delhi
> 
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