Re: [Joelib-devel] Is joelib.jar compatible with applet?

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Hi Joerg

Thank you for reply.

=A3=BEOh, that's the (older) JOELib release, not JOELib2.
The reason why I want to use JOELib is the followings.

I want to make mol file from SMILES Strings, However JOELib2 API
documentation say that
=20
Molecule mol=3Dnew Molecule();
 String smiles=3D"c1cc(OH)cc1";
 if (!JOESmilesParser.smiToMol(mol, smiles, setTitle.toString()))  {
   System.err.println("SMILES entry \"" + smiles + "\" could not be
loaded.");  }  System.out.println(mol.toString());

Since JOESmilesParser is not a class of JOELib2 but JOELib, Using =
JOELib,
JOEMol mol=3Dnew JOEMol();  String smiles=3D"c1cc(OH)cc1";  if
(!JOESmilesParser.smiToMol(mol, smiles, setTitle.toString()))  {
   System.err.println("SMILES entry \"" + smiles + "\" could not be
loaded.");  }  System.out.println(mol.toString());

This works well when I use this as a normal java application.

I also use SMILESParser.smiles2molecule(mol, smiles, =
setTitle.toString())
instead of JOESmilesParser.smiToMol(mol, smiles, setTitle.toString()) =
with
JOELib2, but it does not work.

Thanks in advance,

Takayuki KOTANI

-----Original Message-----
From: joe...@we... [mailto:joe...@we...]
Sent: Saturday, September 09, 2006 7:33 AM
To: t-k...@ni...; Joe...@li...
Subject: AW: [Joelib-devel] Is joelib.jar compatible with applet?

Takayuki,

Oh, that's the (older) JOELib release, not JOELib2.

Please compare carefully those two files and adapt your version, e.g. =
print
the source code.

http://joelib.cvs.sourceforge.net/joelib/joelib/src/wsi/ra/tool/PropertyH=
old
er.java?view=3Dmarkup

versus

http://joelib.cvs.sourceforge.net/joelib/joelib2/src/wsi/ra/tool/BasicPro=
per
tyHolder.java?view=3Dmarkup

Joerg

> -----Urspr=A8=B9ngliche Nachricht-----
> Von: joe...@li... [mailto:joelib-devel-=20
> bo...@li...] Im Auftrag von Takayuki KOTANI
> Gesendet: Freitag, 8. September 2006 04:00
> An: joe...@we...; Joe...@li...
> Betreff: Re: [Joelib-devel] Is joelib.jar compatible with applet?
>=20
> Dear Joerg
>=20
> Thank you for early reply.
>=20
> >Please check those classes and hack them if necessary. I assume that=20
> >some
> of the security settings might not be correct, so you >should maybe=20
> also check Java-Applet security issues, but this is a general=20
> JavaApplet problem and you should check Google and >SUN pages for=20
> that.
>=20
> I am also using cdk.jar and JME.jar as applets and they work well. I=20
> think that problem is not caused by Java-Applet security issues.
>=20
> >Can you enable the debug mode in log4j.properties for
> wsi.ra.tool.BasicResourceLoader wsi.ra.tool.BasicPropertyHolder.
> I tried to modify log4j.properties and the following is log files.
>=20
> [ERROR] wsi.ra.PropertyHolder                    - Propertyfile
> joelib.properties not found.
> java.lang.ExceptionInInitializerError
> 	at chempropapp.setStr(chempropapp.java:44)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
> 	at java.lang.reflect.Method.invoke(Unknown Source)
> 	at sun.plugin.javascript.invoke.JSInvoke.invoke(Unknown Source)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
> 	at java.lang.reflect.Method.invoke(Unknown Source)
> 	at sun.plugin.javascript.JSClassLoader.invoke(Unknown Source)
> 	at sun.plugin.com.MethodDispatcher.invoke(Unknown Source)
> 	at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source)
> 	at sun.plugin.com.DispatchImpl$1.run(Unknown Source)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at sun.plugin.com.DispatchImpl.invoke(Unknown Source) Caused by:=20
> java.security.AccessControlException: access denied=20
> (java.lang.RuntimePermission exitVM)
> 	at java.security.AccessControlContext.checkPermission(Unknown
> Source)
> 	at java.security.AccessController.checkPermission(Unknown Source)
> 	at java.lang.SecurityManager.checkPermission(Unknown Source)
> 	at java.lang.SecurityManager.checkExit(Unknown Source)
> 	at java.lang.Runtime.exit(Unknown Source)
> 	at java.lang.System.exit(Unknown Source)
> 	at wsi.ra.tool.PropertyHolder.instance(PropertyHolder.java:281)
> 	at wsi.ra.tool.PropertyHolder.instance(PropertyHolder.java:258)
> 	at joelib.io.IOTypeHolder.loadFileTypes(IOTypeHolder.java:537)
> 	at joelib.io.IOTypeHolder.instance(IOTypeHolder.java:192)
> 	at joelib.molecule.JOEMol.<clinit>(JOEMol.java:239)
> 	... 16 more
> java.lang.Exception: java.lang.ExceptionInInitializerError
> 	at sun.plugin.com.DispatchImpl.invokeImpl(Unknown Source)
> 	at sun.plugin.com.DispatchImpl$1.run(Unknown Source)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at sun.plugin.com.DispatchImpl.invoke(Unknown Source)
>=20
> Thanks in advance.
>=20
>=20
> Takayuki KOTANI
>=20
>=20
> -----Original Message-----
> From: joe...@we... [mailto:joe...@we...]
> Sent: Friday, September 08, 2006 4:06 AM
> To: t-k...@ni...; Joe...@li...
> Subject: AW: [Joelib-devel] Is joelib.jar compatible with applet?
>=20
> Dear Takayuki,
>=20
> first the Webstart application is deprecated and uses a pretty old=20
> JOELib version, but this is just a site note.
>=20
> Second, all descriptors/features and file formats are defined in the=20
> joelib.properties file. Therefore, this an extremely important=20
> property definitions file.
> I still do not know from the messages provided what is going wrong.=20
> Can you enable the debug mode in log4j.properties for=20
> wsi.ra.tool.BasicResourceLoader wsi.ra.tool.BasicPropertyHolder
>=20
> Those are the relevant classes for getting and loading the properties.
> Usually those classes should be able to get the data from String, URL, =

> and File resources.
>=20
> I had also already some problems with those classes, especially when=20
> working in combination with other projects and dependencies. Anyway,=20
> this is a powerful outsourcing of parameters and avoids hard coded
> (hidden) features, so it is worthwhile solving this.
>=20
> Please check those classes and hack them if necessary. I assume that=20
> some of the security settings might not be correct, so you should=20
> maybe also check Java-Applet security issues, but this is a general=20
> JavaApplet problem and you should check Google and SUN pages for that.
>=20
> Please let me know, if this message was helpful and what the status of =

> your problem is.
>=20
> Joerg
>=20
>=20
>=20
>=20
> ----------------------------------------------------------------------
> --- Using Tomcat but need to do more? Need to support web services,=20
> security?
> Get stuff done quickly with pre-integrated technology to make your job =

> easier Download IBM WebSphere Application Server v.1.0.1 based on=20
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