From: Mateusz Warowny <mmzwarowny@dundee.ac.uk>
Date: Fri, 27 Sep 2019 15:58:56 +0000 (+0100)
Subject: JAL-3066 Automatically discoverable Protein sequence analysis services
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6a7ffd7997c11b84a81acbdd83e462cac76f124b;p=jalview.git

JAL-3066 Automatically discoverable Protein sequence analysis services
---

diff --git a/j11lib/slivka-client.jar b/j11lib/slivka-client.jar
index c990dd8..a8e499a 100644
Binary files a/j11lib/slivka-client.jar and b/j11lib/slivka-client.jar differ
diff --git a/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
index 4fb35a0..184ca2d 100644
--- a/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
@@ -1,16 +1,23 @@
 package jalview.ws.slivkaws;
 
 import jalview.api.FeatureColourI;
+import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.io.AnnotationFile;
 import jalview.ws.api.JobId;
 import jalview.ws.api.SequenceAnnotationServiceI;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 
+import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
+import java.io.IOError;
+import java.io.IOException;
 import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -25,7 +32,7 @@ public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements
 {
   public SlivkaAnnotationServiceInstance(SlivkaClient client, SlivkaService service)
   {
-    super(client, service, "Annotations");
+    super(client, service, "Annotations disorder");
   }
 
   @Override
@@ -71,7 +78,30 @@ public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements
           List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
           Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
   {
-    // TODO Auto-generated method stub
-    return null;
+    RemoteFile annotFile = null;
+    RemoteFile featFile = null;
+    try
+    {
+      List<RemoteFile> files = client.getJobResults(job.getJobId());
+      for (RemoteFile f : files)
+      {
+        if (f.getMimeType().equals("application/jalview-annotations"))
+        {
+          annotFile = f;
+        }
+        else if (f.getMimeType().equals("application/jalview-features"))
+        {
+          featFile = f;
+        }
+      }
+    } catch (IOException e)
+    {
+      throw new IOError(e);
+    }
+    Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
+    BufferedReader in = new BufferedReader(new InputStreamReader(annotFile.getContent()));
+    AnnotationFile f = new AnnotationFile();
+    f.parseAnnotationFrom(aln, null, in);
+    return Arrays.asList(aln.getAlignmentAnnotation());
   }
 }
diff --git a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
index e9d0d53..6b3856a 100644
--- a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
@@ -4,6 +4,7 @@ import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
 import jalview.ws.WSMenuEntryProviderI;
 import jalview.ws.jws2.MsaWSClient;
+import jalview.ws.jws2.SequenceAnnotationWSClient;
 
 import java.awt.event.ActionEvent;
 import java.io.IOError;
@@ -47,9 +48,9 @@ public class SlivkaWSDiscoverer implements Runnable, WSMenuEntryProviderI
   {
     JMenu slivkaMenu = new JMenu("Slivka");
     wsmenu.add(slivkaMenu);
-    JMenu categoryMenu = new JMenu("Alignment");
-    slivkaMenu.add(categoryMenu);
 
+    JMenu alignmentMenu = new JMenu("Sequence Alignment");
+    slivkaMenu.add(alignmentMenu);
     try
     {
       for (SlivkaService service : client.getServices())
@@ -75,7 +76,7 @@ public class SlivkaWSDiscoverer implements Runnable, WSMenuEntryProviderI
                 alignFrame.getViewport().getAlignment().getDataset(), alignFrame);
           }
         });
-        categoryMenu.add(defaultEntry);
+        alignmentMenu.add(defaultEntry);
 
         JMenuItem customEntry = new JMenuItem(String.format("%s with custom parameters", service.label));
         customEntry.addActionListener((ActionEvent evt) -> {
@@ -93,15 +94,53 @@ public class SlivkaWSDiscoverer implements Runnable, WSMenuEntryProviderI
             }
           }
         });
-        categoryMenu.add(customEntry);
+        alignmentMenu.add(customEntry);
 
-        categoryMenu.addSeparator();
+        alignmentMenu.addSeparator();
       }
     } catch (IOException e)
     {
       // TODO Auto-generated catch block
       e.printStackTrace();
     }
+
+    JMenu disorderMenu = new JMenu("Protein sequence analysis");
+    slivkaMenu.add(disorderMenu);
+    try
+    {
+      for (SlivkaService service : client.getServices())
+      {
+        msaClassifier:
+        {
+          for (String classifier : service.classifiers)
+          {
+            if (classifier.contains("Protein sequence analysis"))
+            {
+              break msaClassifier;
+            }
+          }
+          continue;
+        }
+        JMenuItem menuEntry = new JMenuItem(String.format("%s with custom parameters", service.label));
+        disorderMenu.add(menuEntry);
+        SlivkaAnnotationServiceInstance serviceInstance = new SlivkaAnnotationServiceInstance(client, service);
+        menuEntry.addActionListener((ActionEvent evt) -> {
+          try
+          {
+            SlivkaParamSet paramSet = new SlivkaParamSet(service);
+            SequenceAnnotationWSClient client = new SequenceAnnotationWSClient();
+            client.initSequenceAnnotationWSClient(serviceInstance, alignFrame, paramSet, true);
+          } catch (IOException e)
+          {
+            throw new IOError(e);
+          }
+
+        });
+      }
+    } catch (IOException e)
+    {
+      throw new IOError(e);
+    }
   }
 
   @Override