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JAL-1365 refactored core methods from RNAAliFold and AACon service clients to a commo...
[jalview.git]
/
src
/
jalview
/
ws
/
jws2
/
RNAalifoldClient.java
diff --git
a/src/jalview/ws/jws2/RNAalifoldClient.java
b/src/jalview/ws/jws2/RNAalifoldClient.java
index
d86f15a
..
b8b30c5
100644
(file)
--- a/
src/jalview/ws/jws2/RNAalifoldClient.java
+++ b/
src/jalview/ws/jws2/RNAalifoldClient.java
@@
-21,6
+21,12
@@
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
import compbio.metadata.Argument;
import compbio.data.sequence.Score;
import compbio.metadata.Argument;
+/**
+ * Client for the JABA RNA Alifold Service
+ * @author daluke - Daniel Barton
+ *
+ */
+
public class RNAalifoldClient extends JabawsAlignCalcWorker implements
AlignCalcWorkerI
{
public class RNAalifoldClient extends JabawsAlignCalcWorker implements
AlignCalcWorkerI
{
@@
-38,24
+44,25
@@
public class RNAalifoldClient extends JabawsAlignCalcWorker implements
{
super(sh, alignFrame, preset, paramset);
{
super(sh, alignFrame, preset, paramset);
- if (arguments == null)
- arguments = new ArrayList<Argument>();
+ //if (arguments == null)
+ // arguments = new ArrayList<Argument>();
af = alignFrame;
methodName = sh.serviceType;
af = alignFrame;
methodName = sh.serviceType;
-
+ alignedSeqs=true;
+ submitGaps=true;
nucleotidesAllowed = true;
proteinAllowed = false;
initViewportParams();
}
nucleotidesAllowed = true;
proteinAllowed = false;
initViewportParams();
}
+
+ public String getCalcId()
+ {
+ return CALC_ID;
+ }
+ private static String CALC_ID="jalview.ws.jws2.RNAalifoldClient";
- protected void initViewportParams()
{
{
- ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
- getCalcId(),
- new AAConSettings(true, service, this.preset,
- (arguments != null) ? JabaParamStore
- .getJwsArgsfromJaba(arguments) : null), true);
}
@Override
}
@Override
@@
-332,10
+339,4
@@
public class RNAalifoldClient extends JabawsAlignCalcWorker implements
char ss = (Pattern.matches(regex, Character.toString(chr))) ? 'S' : ' ';
return ss;
}
char ss = (Pattern.matches(regex, Character.toString(chr))) ? 'S' : ' ';
return ss;
}
-
- public String getCalcId()
- {
- return SequenceAnnotationWSClient.AAConCalcId;
- }
-
}
}