Re: Help with Java version of Readseq
On 12/23/2013 09:01 AM, Andreas Tille wrote:
> Hi Olivier,
>
> On Mon, Dec 23, 2013 at 08:27:03AM +0100, Olivier Sallou wrote:
>>> and rdp-classifier in turn is recommended by qiime. When inspecting
>>> the build.xml of readseq2 it says:
>>>
>>> need these libs or replace w/ others
>>> 218510 Jul 25 1999 ibm-xml4j-min.jar
>>> 15054 Jul 17 1999 orgxml.jar
>>>
>>> while orgxml.jar is no problem since its classes seem to be even in
>>> OpenJDK 7 I have no idea how to replace ibm-xml4j-min.jar with others.
>> Do you know which classes are used by the code in ibm-xml4j ?
> I have no idea about this.
There is no direct code using it, but using generic xml APIs.
I tried the following patch with libxerces2-java and it worked for
compilation (did not test runtime)
--- a/build.xml
+++ b/build.xml
@@ -46,8 +46,8 @@
! UPDATE THESE to newer xml jars ; also include in readseq.jar
-->
- <property name="orgxml.jar" value="${basedir}/lib/orgxml.jar"/>
- <property name="xml.jar" value="${basedir}/lib/ibm-xml4j-min.jar"/>
+ <property name="orgxml.jar" value="/usr/share/java/xmlParserAPIs.jar"/>
+ <property name="xml.jar" value="/usr/share/java/xercesImpl.jar"/>
<!-- ==================== Compilation Classpath
=========================== -->
>
>> Some hints on the web says that xerces3 should match (more or less) this
>> lib, but we should check exact usage.
> When checking
>
> http://ftp-master.debian.org/users/twerner/jar-content.txt.gz
>
> some clases of xerces sounded similar. I have no better hint for you.
>
> Kind regards
>
> Andreas.
>
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
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