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JAL-3070 rename AbstractJabaCalcWorker to SeqAnnotationServiceCalcWorker
author
Jim Procter
<jprocter@issues.jalview.org>
Mon, 23 Sep 2019 09:36:19 +0000
(10:36 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Mon, 23 Sep 2019 09:36:19 +0000
(10:36 +0100)
src/jalview/ws/api/SequenceAnnotationServiceI.java
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src/jalview/ws/jws2/Jws2ClientFactory.java
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src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
[moved from
src/jalview/ws/jws2/AbstractJabaCalcWorker.java
with 98% similarity]
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src/jalview/ws/jws2/SequenceAnnotationWSClient.java
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src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java
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src/jalview/ws/jws2/jabaws2/JabawsMsaInterfaceAlignCalcWorker.java
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test/jalview/ws/jabaws/DisorderAnnotExportImport.java
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test/jalview/ws/jabaws/RNAStructExportImport.java
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diff --git
a/src/jalview/ws/api/SequenceAnnotationServiceI.java
b/src/jalview/ws/api/SequenceAnnotationServiceI.java
index
d0965e5
..
a224bac
100644
(file)
--- a/
src/jalview/ws/api/SequenceAnnotationServiceI.java
+++ b/
src/jalview/ws/api/SequenceAnnotationServiceI.java
@@
-3,7
+3,7
@@
package jalview.ws.api;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.ws.gui.AnnotationWsJob;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.ws.gui.AnnotationWsJob;
-import jalview.ws.jws2.AbstractJabaCalcWorker;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
@@
-34,7
+34,7
@@
public interface SequenceAnnotationServiceI extends JalviewWebServiceI
* @return
*/
List<AlignmentAnnotation> getAlignmentAnnotation(AnnotationWsJob running,
* @return
*/
List<AlignmentAnnotation> getAlignmentAnnotation(AnnotationWsJob running,
- AbstractJabaCalcWorker abstractJabaCalcWorker) throws Throwable;
+ SeqAnnotationServiceCalcWorker abstractJabaCalcWorker) throws Throwable;
}
}
diff --git
a/src/jalview/ws/jws2/Jws2ClientFactory.java
b/src/jalview/ws/jws2/Jws2ClientFactory.java
index
2a3b4a5
..
99edbec
100644
(file)
--- a/
src/jalview/ws/jws2/Jws2ClientFactory.java
+++ b/
src/jalview/ws/jws2/Jws2ClientFactory.java
@@
-55,7
+55,7
@@
public class Jws2ClientFactory
.getRegisteredWorkersOfClass(aaui.getClient());
if (aaconClient != null && aaconClient.size() > 0)
{
.getRegisteredWorkersOfClass(aaui.getClient());
if (aaconClient != null && aaconClient.size() > 0)
{
- AbstractJabaCalcWorker worker = (AbstractJabaCalcWorker) aaconClient
+ SeqAnnotationServiceCalcWorker worker = (SeqAnnotationServiceCalcWorker) aaconClient
.get(0);
if (!worker.service.getHostURL().equals(service.getHostURL()))
{
.get(0);
if (!worker.service.getHostURL().equals(service.getHostURL()))
{
@@
-138,14
+138,14
@@
public class Jws2ClientFactory
}
List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
.getCalcManager().getRegisteredWorkersOfClass(
}
List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
.getCalcManager().getRegisteredWorkersOfClass(
- AbstractJabaCalcWorker.class);
+ SeqAnnotationServiceCalcWorker.class);
boolean serviceEnabled = false;
if (aaconClient != null)
{
for (AlignCalcWorkerI _worker : aaconClient)
{
boolean serviceEnabled = false;
if (aaconClient != null)
{
for (AlignCalcWorkerI _worker : aaconClient)
{
- AbstractJabaCalcWorker worker = (AbstractJabaCalcWorker) _worker;
+ SeqAnnotationServiceCalcWorker worker = (SeqAnnotationServiceCalcWorker) _worker;
// this could be cleaner ?
if (worker.hasService()
&& aaui.getClient()
// this could be cleaner ?
if (worker.hasService()
&& aaui.getClient()
diff --git
a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
b/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
similarity index 98%
rename from
src/jalview/ws/jws2/AbstractJabaCalcWorker.java
rename to
src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
index
fae8089
..
6793f1e
100644
(file)
--- a/
src/jalview/ws/jws2/AbstractJabaCalcWorker.java
+++ b/
src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
@@
-52,7
+52,7
@@
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.List;
import java.util.Map;
-public class AbstractJabaCalcWorker extends AlignCalcWorker
+public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
implements WSAnnotationCalcManagerI
{
implements WSAnnotationCalcManagerI
{
@@
-151,13
+151,13
@@
public class AbstractJabaCalcWorker extends AlignCalcWorker
return gapMap;
}
return gapMap;
}
- public AbstractJabaCalcWorker(AlignViewportI alignViewport,
+ public SeqAnnotationServiceCalcWorker(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
super(alignViewport, alignPanel);
}
AlignmentViewPanel alignPanel)
{
super(alignViewport, alignPanel);
}
- public AbstractJabaCalcWorker(Jws2Instance service, AlignFrame alignFrame,
+ public SeqAnnotationServiceCalcWorker(Jws2Instance service, AlignFrame alignFrame,
WsParamSetI preset, List<ArgumentI> paramset)
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
WsParamSetI preset, List<ArgumentI> paramset)
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
diff --git
a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index
58478d6
..
bf5dc23
100644
(file)
--- a/
src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/
src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@
-84,14
+84,14
@@
public class SequenceAnnotationWSClient extends Jws2Client
List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
.getCalcManager()
List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
.getCalcManager()
- .getRegisteredWorkersOfClass(AbstractJabaCalcWorker.class);
+ .getRegisteredWorkersOfClass(SeqAnnotationServiceCalcWorker.class);
- AbstractJabaCalcWorker worker = null;
+ SeqAnnotationServiceCalcWorker worker = null;
if (clnts != null)
{
for (AlignCalcWorkerI _worker : clnts)
{
if (clnts != null)
{
for (AlignCalcWorkerI _worker : clnts)
{
- worker = (AbstractJabaCalcWorker) _worker;
+ worker = (SeqAnnotationServiceCalcWorker) _worker;
if (worker.hasService()
&& worker.getService().getClass().equals(clientClass))
{
if (worker.hasService()
&& worker.getService().getClass().equals(clientClass))
{
@@
-108,7
+108,7
@@
public class SequenceAnnotationWSClient extends Jws2Client
}
try
{
}
try
{
- worker = new AbstractJabaCalcWorker(sh, alignFrame, this.preset,
+ worker = new SeqAnnotationServiceCalcWorker(sh, alignFrame, this.preset,
paramset);
} catch (Exception x)
{
paramset);
} catch (Exception x)
{
@@
-149,7
+149,7
@@
public class SequenceAnnotationWSClient extends Jws2Client
}
alignFrame.getViewport().getCalcManager().startWorker(
}
alignFrame.getViewport().getCalcManager().startWorker(
- new AbstractJabaCalcWorker(sh, alignFrame, preset, paramset));
+ new SeqAnnotationServiceCalcWorker(sh, alignFrame, preset, paramset));
}
}
}
}
diff --git
a/src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java
b/src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java
index
3c269c4
..
8acf64f
100644
(file)
--- a/
src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java
+++ b/
src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java
@@
-8,7
+8,7
@@
import jalview.util.MessageManager;
import jalview.ws.api.JobId;
import jalview.ws.api.SequenceAnnotationServiceI;
import jalview.ws.gui.AnnotationWsJob;
import jalview.ws.api.JobId;
import jalview.ws.api.SequenceAnnotationServiceI;
import jalview.ws.gui.AnnotationWsJob;
-import jalview.ws.jws2.AbstractJabaCalcWorker;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.JabaPreset;
import jalview.ws.params.ArgumentI;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.JabaPreset;
import jalview.ws.params.ArgumentI;
@@
-108,7
+108,7
@@
public abstract class JabawsAnnotationInstance
@Override
public List<AlignmentAnnotation> getAlignmentAnnotation(
AnnotationWsJob running,
@Override
public List<AlignmentAnnotation> getAlignmentAnnotation(
AnnotationWsJob running,
- AbstractJabaCalcWorker abstractJabaCalcWorker) throws Throwable
+ SeqAnnotationServiceCalcWorker abstractJabaCalcWorker) throws Throwable
{
if (scoremanager == null)
{
{
if (scoremanager == null)
{
diff --git
a/src/jalview/ws/jws2/jabaws2/JabawsMsaInterfaceAlignCalcWorker.java
b/src/jalview/ws/jws2/jabaws2/JabawsMsaInterfaceAlignCalcWorker.java
index
aff7ad6
..
edcc05c
100644
(file)
--- a/
src/jalview/ws/jws2/jabaws2/JabawsMsaInterfaceAlignCalcWorker.java
+++ b/
src/jalview/ws/jws2/jabaws2/JabawsMsaInterfaceAlignCalcWorker.java
@@
-21,14
+21,14
@@
package jalview.ws.jws2.jabaws2;
import jalview.gui.AlignFrame;
package jalview.ws.jws2.jabaws2;
import jalview.gui.AlignFrame;
-import jalview.ws.jws2.AbstractJabaCalcWorker;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import java.util.List;
public abstract class JabawsMsaInterfaceAlignCalcWorker
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import java.util.List;
public abstract class JabawsMsaInterfaceAlignCalcWorker
- extends AbstractJabaCalcWorker
+ extends SeqAnnotationServiceCalcWorker
{
public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,
{
public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,
diff --git
a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
index
3e3a06d
..
de72020
100644
(file)
--- a/
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@
-32,7
+32,7
@@
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.AbstractJabaCalcWorker;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.jabaws2.Jws2Instance;
@@
-65,7
+65,7
@@
public class DisorderAnnotExportImport
public static List<Jws2Instance> iupreds;
public static List<Jws2Instance> iupreds;
- jalview.ws.jws2.AbstractJabaCalcWorker disorderClient;
+ jalview.ws.jws2.SeqAnnotationServiceCalcWorker disorderClient;
public static jalview.gui.AlignFrame af = null;
public static jalview.gui.AlignFrame af = null;
@@
-114,7
+114,7
@@
public class DisorderAnnotExportImport
@Test(groups = { "External", "Network" })
public void testDisorderAnnotExport()
{
@Test(groups = { "External", "Network" })
public void testDisorderAnnotExport()
{
- disorderClient = new AbstractJabaCalcWorker(iupreds.get(0), af, null,
+ disorderClient = new SeqAnnotationServiceCalcWorker(iupreds.get(0), af, null,
null);
af.getViewport().getCalcManager().startWorker(disorderClient);
do
null);
af.getViewport().getCalcManager().startWorker(disorderClient);
do
diff --git
a/test/jalview/ws/jabaws/RNAStructExportImport.java
b/test/jalview/ws/jabaws/RNAStructExportImport.java
index
4af8086
..
25d015a
100644
(file)
--- a/
test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/
test/jalview/ws/jabaws/RNAStructExportImport.java
@@
-33,7
+33,7
@@
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.project.Jalview2XML;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.project.Jalview2XML;
-import jalview.ws.jws2.AbstractJabaCalcWorker;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.SequenceAnnotationWSClient;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.SequenceAnnotationWSClient;
@@
-79,7
+79,7
@@
public class RNAStructExportImport
public static Jws2Instance rnaalifoldws;
public static Jws2Instance rnaalifoldws;
- AbstractJabaCalcWorker alifoldClient;
+ SeqAnnotationServiceCalcWorker alifoldClient;
public static jalview.gui.AlignFrame af = null;
public static jalview.gui.AlignFrame af = null;
@@
-155,7
+155,7
@@
public class RNAStructExportImport
public void testRNAAliFoldValidStructure()
{
public void testRNAAliFoldValidStructure()
{
- alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
+ alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
null);
af.getViewport().getCalcManager().startWorker(alifoldClient);
null);
af.getViewport().getCalcManager().startWorker(alifoldClient);
@@
-189,7
+189,7
@@
public class RNAStructExportImport
public void testRNAStructExport()
{
public void testRNAStructExport()
{
- alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
+ alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
null);
af.getViewport().getCalcManager().startWorker(alifoldClient);
null);
af.getViewport().getCalcManager().startWorker(alifoldClient);
@@
-283,7
+283,7
@@
public class RNAStructExportImport
opts.add(rg);
}
}
opts.add(rg);
}
}
- alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
+ alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
JabaParamStore.getJwsArgsfromJaba(opts));
af.getViewport().getCalcManager().startWorker(alifoldClient);
JabaParamStore.getJwsArgsfromJaba(opts));
af.getViewport().getCalcManager().startWorker(alifoldClient);