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JAL-3725 exclude stop codon from CDS-to-protein mapping
[jalview.git]
/
src
/
jalview
/
ws
/
jws2
/
jabaws2
/
Jws2Instance.java
diff --git
a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
index
61ff7eb
..
e092192
100644
(file)
--- a/
src/jalview/ws/jws2/jabaws2/Jws2Instance.java
+++ b/
src/jalview/ws/jws2/jabaws2/Jws2Instance.java
@@
-38,7
+38,7
@@
import compbio.data.msa.SequenceAnnotation;
import compbio.metadata.PresetManager;
import compbio.metadata.RunnerConfig;
import compbio.metadata.PresetManager;
import compbio.metadata.RunnerConfig;
-public class Jws2Instance
+public class Jws2Instance implements AutoCloseable
{
public String hosturl;
{
public String hosturl;
@@
-159,25
+159,24
@@
public class Jws2Instance
}
throw new Error(MessageManager.formatMessage(
"error.implementation_error_runner_config_not_available",
}
throw new Error(MessageManager.formatMessage(
"error.implementation_error_runner_config_not_available",
- new String[] { serviceType, service.getClass().toString() }));
+ new String[]
+ { serviceType, service.getClass().toString() }));
}
@Override
}
@Override
- protected void finalize() throws Throwable
+ public void close()
{
if (service != null)
{
try
{
{
if (service != null)
{
try
{
- Closeable svc = (Closeable) service;
- service = null;
- svc.close();
- } catch (Exception e)
+ ((Closeable) service).close();
+ } catch (Throwable t)
{
{
+ // ignore
}
}
- ;
}
}
- super.finalize();
+ // super.finalize();
}
public ParamDatastoreI getParamStore()
}
public ParamDatastoreI getParamStore()
@@
-204,7
+203,8
@@
public class Jws2Instance
// this is only valid for Jaba 1.0 - this formula might have to change!
return hosturl
+ (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? ""
// this is only valid for Jaba 1.0 - this formula might have to change!
return hosturl
+ (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? ""
- : "/") + serviceType;
+ : "/")
+ + serviceType;
}
private boolean hasParams = false, lookedForParams = false;
}
private boolean hasParams = false, lookedForParams = false;