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JAL-2089 patch broken merge to master for Release 2.10.0b1
[jalview.git]
/
src
/
jalview
/
ws
/
jws2
/
JPred301Client.java
diff --git
a/src/jalview/ws/jws2/JPred301Client.java
b/src/jalview/ws/jws2/JPred301Client.java
index
db70fa0
..
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)
@@
-128,8
+127,7
@@
public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
String[] k = jpredRowLabels.get(fsq.getId());
if (k == null)
{
String[] k = jpredRowLabels.get(fsq.getId());
if (k == null)
{
- k = new String[]
- { fsq.getId(), "JNet Output" };
+ k = new String[] { fsq.getId(), "JNet Output" };
}
if (fsq.getId().startsWith("JNETSOL"))
{
}
if (fsq.getId().startsWith("JNETSOL"))
{
@@
-142,7
+140,8
@@
public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
{
sol[spos] = '0';
}
{
sol[spos] = '0';
}
- if (vseq[spos] == 'B' && (sol[spos]=='0' || sol[spos] < amnt))
+ if (vseq[spos] == 'B'
+ && (sol[spos] == '0' || sol[spos] < amnt))
{
sol[spos] = amnt;
}
{
sol[spos] = amnt;
}
@@
-252,7
+251,7
@@
public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
try
{
elm[i] = new Annotation("" + annot, "" + annot, annot,
try
{
elm[i] = new Annotation("" + annot, "" + annot, annot,
- Integer.valueOf(""+annot));
+ Integer.valueOf("" + annot));
} catch (Exception x)
{
System.err.println("Expected numeric value in character '"
} catch (Exception x)
{
System.err.println("Expected numeric value in character '"