From: Mateusz Warowny <mmzwarowny@dundee.ac.uk>
Date: Tue, 19 Oct 2021 13:40:22 +0000 (+0200)
Subject: JAL-3878 Add annotation operations to slivka discoverer.
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=5286575417e72e6b9323bfa365eca1b022bdbe1d

JAL-3878 Add annotation operations to slivka discoverer.
---

diff --git a/src/jalview/ws2/slivka/SlivkaWSDiscoverer.java b/src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
index b55035b..c0c7502 100644
--- a/src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
+++ b/src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
@@ -9,6 +9,7 @@ import java.util.concurrent.*;
 import jalview.bin.Cache;
 import jalview.ws2.*;
 import jalview.ws2.operations.AlignmentOperation;
+import jalview.ws2.operations.AnnotationOperation;
 import jalview.ws2.operations.Operation;
 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
@@ -166,11 +167,26 @@ public class SlivkaWSDiscoverer implements WebServiceDiscoverer
             Operation op = null;
             switch (path[path.length - 1].toLowerCase())
             {
+            case "sequence alignment analysis (conservation)":
+              AnnotationOperation anop;
+              op = anop = new AnnotationOperation(instance,
+                  instance::getAnnotations, instance::getFeaturesFile, "Conservation");
+              anop.setAlignmentAnalysis(true);
+              anop.setInteractive(true);
+              break;
+            case "protein sequence analysis":
+              op = new AnnotationOperation(instance, instance::getAnnotations,
+                  instance::getFeaturesFile, "Protein Disorder");
+              break;
             case "multiple sequence alignment":
               op = new AlignmentOperation(instance, instance::getAlignment);
+              break;
             }
             if (op != null)
+            {
               instance.addOperation(op);
+              break;
+            }
           }
         }
         if (instance.operations.size() > 0)