Merge branch 'tasks/JAL-3070_wsinterfaces' into alpha/JAL-3362_Jalview_212_alpha

[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 f9e597f..7d6d341 100644 (file)
--- a/src/jalview/ws/jws2/RNAalifoldClient.java
+++ b/src/jalview/ws/jws2/RNAalifoldClient.java
@@ -25,6 +25,7 @@ import jalview.datamodel.Annotation;
 import jalview.gui.AlignFrame;
 import jalview.util.MessageManager;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws.uimodel.AlignAnalysisUIText;
 
@@ -40,7 +41,6 @@ import compbio.data.sequence.RNAStructReader.AlifoldResult;
 import compbio.data.sequence.RNAStructScoreManager;
 import compbio.data.sequence.Range;
 import compbio.data.sequence.Score;
-import compbio.metadata.Argument;
 
 /**
  * Client for the JABA RNA Alifold Service
@@ -61,11 +61,11 @@ public class RNAalifoldClient extends JabawsCalcWorker
   boolean bpScores;
 
   public RNAalifoldClient(Jws2Instance sh, AlignFrame alignFrame,
-          WsParamSetI preset, List<Argument> paramset)
+          WsParamSetI preset, List<ArgumentI> paramset)
   {
     super(sh, alignFrame, preset, paramset);
     af = alignFrame;
-    methodName = sh.serviceType;
+    methodName = sh.getName();
     alignedSeqs = true;
     submitGaps = true;
     nucleotidesAllowed = true;
@@ -112,7 +112,7 @@ public class RNAalifoldClient extends JabawsCalcWorker
     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
     {
 
-      List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
+      List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
 
       // Unpack the ScoreManager
       List<String> structs = ((RNAStructScoreManager) scoremanager)
@@ -231,7 +231,7 @@ public class RNAalifoldClient extends JabawsCalcWorker
 
       // The base pair probabilities are stored in a set in scoreholder. we want
       // a map
-      LinkedHashMap<Range, Float> basePairs = new LinkedHashMap<Range, Float>();
+      LinkedHashMap<Range, Float> basePairs = new LinkedHashMap<>();
       for (Score score : data)
       {
         // The Score objects contain a set of size one containing the range and
@@ -377,7 +377,7 @@ public class RNAalifoldClient extends JabawsCalcWorker
   private LinkedHashMap<Range, Float> isContact(
           LinkedHashMap<Range, Float> basePairs, int i)
   {
-    LinkedHashMap<Range, Float> contacts = new LinkedHashMap<Range, Float>();
+    LinkedHashMap<Range, Float> contacts = new LinkedHashMap<>();
 
     for (Range contact : basePairs.keySet())
     {