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JAL-2068 redundant implements clauses removed
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 22 Apr 2016 14:23:05 +0000
(15:23 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 22 Apr 2016 14:23:05 +0000
(15:23 +0100)
src/jalview/workers/ConsensusThread.java
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src/jalview/workers/ConservationThread.java
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src/jalview/workers/StrucConsensusThread.java
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src/jalview/ws/jws2/AADisorderClient.java
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src/jalview/ws/jws2/JPred301Client.java
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src/jalview/ws/jws2/RNAalifoldClient.java
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diff --git
a/src/jalview/workers/ConsensusThread.java
b/src/jalview/workers/ConsensusThread.java
index
a8698e6
..
14e2a31
100644
(file)
--- a/
src/jalview/workers/ConsensusThread.java
+++ b/
src/jalview/workers/ConsensusThread.java
@@
-21,7
+21,6
@@
package jalview.workers;
import jalview.analysis.AAFrequency;
package jalview.workers;
import jalview.analysis.AAFrequency;
-import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
@@
-32,8
+31,7
@@
import jalview.schemes.ColourSchemeI;
import java.util.Hashtable;
import java.util.Hashtable;
-public class ConsensusThread extends AlignCalcWorker implements
- AlignCalcWorkerI
+public class ConsensusThread extends AlignCalcWorker
{
public ConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
public ConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
diff --git
a/src/jalview/workers/ConservationThread.java
b/src/jalview/workers/ConservationThread.java
index
236bccf
..
1075e4d
100644
(file)
--- a/
src/jalview/workers/ConservationThread.java
+++ b/
src/jalview/workers/ConservationThread.java
@@
-21,7
+21,6
@@
package jalview.workers;
import jalview.analysis.Conservation;
package jalview.workers;
import jalview.analysis.Conservation;
-import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
@@
-30,8
+29,7
@@
import jalview.datamodel.AlignmentI;
import java.util.ArrayList;
import java.util.List;
import java.util.ArrayList;
import java.util.List;
-public class ConservationThread extends AlignCalcWorker implements
- AlignCalcWorkerI
+public class ConservationThread extends AlignCalcWorker
{
private int ConsPercGaps = 25; // JBPNote : This should be a configurable
{
private int ConsPercGaps = 25; // JBPNote : This should be a configurable
diff --git
a/src/jalview/workers/StrucConsensusThread.java
b/src/jalview/workers/StrucConsensusThread.java
index
e0b3833
..
3483dac
100644
(file)
--- a/
src/jalview/workers/StrucConsensusThread.java
+++ b/
src/jalview/workers/StrucConsensusThread.java
@@
-21,7
+21,6
@@
package jalview.workers;
import jalview.analysis.StructureFrequency;
package jalview.workers;
import jalview.analysis.StructureFrequency;
-import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
@@
-31,8
+30,7
@@
import jalview.datamodel.SequenceI;
import java.util.Hashtable;
import java.util.Hashtable;
-public class StrucConsensusThread extends AlignCalcWorker implements
- AlignCalcWorkerI
+public class StrucConsensusThread extends AlignCalcWorker
{
public StrucConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
public StrucConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
diff --git
a/src/jalview/ws/jws2/AADisorderClient.java
b/src/jalview/ws/jws2/AADisorderClient.java
index
f929b1e
..
f4b1c31
100644
(file)
--- a/
src/jalview/ws/jws2/AADisorderClient.java
+++ b/
src/jalview/ws/jws2/AADisorderClient.java
@@
-20,7
+20,6
@@
*/
package jalview.ws.jws2;
*/
package jalview.ws.jws2;
-import jalview.api.AlignCalcWorkerI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.GraphLine;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.GraphLine;
@@
-46,8
+45,7
@@
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager.ScoreHolder;
import compbio.metadata.Argument;
import compbio.data.sequence.ScoreManager.ScoreHolder;
import compbio.metadata.Argument;
-public class AADisorderClient extends JabawsCalcWorker implements
- AlignCalcWorkerI
+public class AADisorderClient extends JabawsCalcWorker
{
private static final String THRESHOLD = "THRESHOLD";
{
private static final String THRESHOLD = "THRESHOLD";
diff --git
a/src/jalview/ws/jws2/JPred301Client.java
b/src/jalview/ws/jws2/JPred301Client.java
index
e4d6329
..
c15f256
100644
(file)
--- a/
src/jalview/ws/jws2/JPred301Client.java
+++ b/
src/jalview/ws/jws2/JPred301Client.java
@@
-20,7
+20,6
@@
*/
package jalview.ws.jws2;
*/
package jalview.ws.jws2;
-import jalview.api.AlignCalcWorkerI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.gui.AlignFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.gui.AlignFrame;
@@
-43,9
+42,7
@@
import compbio.data.sequence.JpredAlignment;
import compbio.metadata.Argument;
public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
import compbio.metadata.Argument;
public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
- implements AlignCalcWorkerI
{
{
-
/**
*
* @return default args for this service when run as dynamic web service
/**
*
* @return default args for this service when run as dynamic web service
@@
-87,6
+84,7
@@
public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
return (seqs.size() > 1);
}
return (seqs.size() > 1);
}
+ @Override
public String getServiceActionText()
{
return "calculating consensus secondary structure prediction using JPred service";
public String getServiceActionText()
{
return "calculating consensus secondary structure prediction using JPred service";
@@
-112,6
+110,7
@@
public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
* update the consensus annotation from the sequence profile data using
* current visualization settings.
*/
* update the consensus annotation from the sequence profile data using
* current visualization settings.
*/
+ @Override
public void updateResultAnnotation(boolean immediate)
{
if (immediate || !calcMan.isWorking(this) && msascoreset != null)
public void updateResultAnnotation(boolean immediate)
{
if (immediate || !calcMan.isWorking(this) && msascoreset != null)
diff --git
a/src/jalview/ws/jws2/RNAalifoldClient.java
b/src/jalview/ws/jws2/RNAalifoldClient.java
index
41aa223
..
9ca6d2e
100644
(file)
--- a/
src/jalview/ws/jws2/RNAalifoldClient.java
+++ b/
src/jalview/ws/jws2/RNAalifoldClient.java
@@
-20,7
+20,6
@@
*/
package jalview.ws.jws2;
*/
package jalview.ws.jws2;
-import jalview.api.AlignCalcWorkerI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.gui.AlignFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.gui.AlignFrame;
@@
-50,8
+49,7
@@
import compbio.metadata.Argument;
*
*/
*
*/
-public class RNAalifoldClient extends JabawsCalcWorker implements
- AlignCalcWorkerI
+public class RNAalifoldClient extends JabawsCalcWorker
{
String methodName;
{
String methodName;
@@
-75,6
+73,7
@@
public class RNAalifoldClient extends JabawsCalcWorker implements
initViewportParams();
}
initViewportParams();
}
+ @Override
public String getCalcId()
{
return CALC_ID;
public String getCalcId()
{
return CALC_ID;