JAL-3899 Update usages of uniquify and deuniquify.

[jalview.git] / src / jalview / ws / jws1 / JPredClient.java

diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java
index 3b7bdb6..4af83f1 100644 (file)
--- a/src/jalview/ws/jws1/JPredClient.java
+++ b/src/jalview/ws/jws1/JPredClient.java
@@ -21,6 +21,7 @@
 package jalview.ws.jws1;
 
 import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SeqCigar;
@@ -34,6 +35,7 @@ import jalview.util.MessageManager;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.util.Hashtable;
+import java.util.Map;
 
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
@@ -127,8 +129,8 @@ public class JPredClient extends WS1Client
         aln[i] = msf[i].getSeq('-');
       }
 
-      Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
-              true);
+      Map<String, SequenceInfo> SequenceInfo = 
+          jalview.analysis.SeqsetUtils.uniquify(aln, true);
       if (viewonly)
       {
         // Remove hidden regions from sequence objects.
@@ -161,7 +163,7 @@ public class JPredClient extends WS1Client
               + (viewonly ? "visible " : "") + "sequence " + seq.getName()
               + " from " + title;
       String seqname = seq.getName();
-      Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
+      SequenceInfo SequenceInfo = jalview.analysis.SeqsetUtils
               .SeqCharacterHash(seq);
       if (viewonly)
       {
@@ -249,8 +251,8 @@ public class JPredClient extends WS1Client
       aln[i] = new jalview.datamodel.Sequence(msf[i]);
     }
 
-    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
-            true);
+    Map<String, SequenceInfo> SequenceInfo = 
+        jalview.analysis.SeqsetUtils.uniquify(aln, true);
 
     Jpred server = locateWebService();
     if (server == null)
@@ -278,7 +280,7 @@ public class JPredClient extends WS1Client
     String altitle = "JPred prediction for sequence " + seq.getName()
             + " from " + title;
 
-    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
+    SequenceInfo SequenceInfo = jalview.analysis.SeqsetUtils
             .SeqCharacterHash(seq);
 
     Jpred server = locateWebService();
@@ -304,7 +306,7 @@ public class JPredClient extends WS1Client
     WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
 
     WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
-            WebServiceReference, true);
+            WebServiceReference, Desktop.FRAME_MAKE_VISIBLE);
 
     return wsInfo;
   }
@@ -323,7 +325,7 @@ public class JPredClient extends WS1Client
 
     } catch (Exception ex)
     {
-      JvOptionPane.showMessageDialog(Desktop.desktop,
+      JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
               MessageManager.formatMessage(
                       "label.secondary_structure_prediction_service_couldnt_be_located",
                       new String[]