X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FJPredClient.java;h=e9c2aeaf5cda98c39a05fcb9f51cf0d183db2346;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=65847e6db6a06e2d9f80ed70fde474f5c8997295;hpb=cd4e2687751aab1c9c5974e6966e610a3332236b;p=jalview.git

diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java
index 65847e6..e9c2aea 100644
--- a/src/jalview/ws/jws1/JPredClient.java
+++ b/src/jalview/ws/jws1/JPredClient.java
@@ -20,6 +20,8 @@
  */
 package jalview.ws.jws1;
 
+import java.util.Locale;
+
 import jalview.analysis.AlignSeq;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentView;
@@ -59,9 +61,8 @@ public class JPredClient extends WS1Client
    * @param viewonly
    *          TODO
    */
-  public JPredClient(ext.vamsas.ServiceHandle sh, String title,
-          boolean msa, AlignmentView alview, AlignFrame parentFrame,
-          boolean viewonly)
+  public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa,
+          AlignmentView alview, AlignFrame parentFrame, boolean viewonly)
   {
     super();
     wsInfo = setWebService(sh);
@@ -154,9 +155,8 @@ public class JPredClient extends WS1Client
     {
       if (!msa && msf.length > 1)
       {
-        throw new Error(
-                MessageManager
-                        .getString("error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
+        throw new Error(MessageManager.getString(
+                "error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
       }
 
       String altitle = getPredictionName(WebServiceName) + " for "
@@ -185,8 +185,8 @@ public class JPredClient extends WS1Client
 
   private String getPredictionName(String webServiceName)
   {
-    if (webServiceName.toLowerCase().indexOf(
-            "secondary structure prediction") > -1)
+    if (webServiceName.toLowerCase(Locale.ROOT)
+            .indexOf("secondary structure prediction") > -1)
     {
       return webServiceName;
     }
@@ -243,7 +243,8 @@ public class JPredClient extends WS1Client
 
     wsInfo.setProgressText("Job details for MSA based prediction (" + title
             + ") on sequence :\n>" + seq.getName() + "\n"
-            + AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) + "\n");
+            + AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+            + "\n");
     SequenceI aln[] = new SequenceI[msf.length];
     for (int i = 0, j = msf.length; i < j; i++)
     {
@@ -274,7 +275,8 @@ public class JPredClient extends WS1Client
     }
     wsInfo.setProgressText("Job details for prediction on sequence :\n>"
             + seq.getName() + "\n"
-            + AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) + "\n");
+            + AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+            + "\n");
     String altitle = "JPred prediction for sequence " + seq.getName()
             + " from " + title;
 
@@ -323,21 +325,17 @@ public class JPredClient extends WS1Client
 
     } catch (Exception ex)
     {
-      JvOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
-                      MessageManager
-                              .formatMessage(
-                                      "label.secondary_structure_prediction_service_couldnt_be_located",
-                                      new String[] { WebServiceName, WsURL }),
-                      MessageManager
-                              .getString("label.internal_jalview_error"),
-                      JvOptionPane.WARNING_MESSAGE);
-      wsInfo.setProgressText(MessageManager
-              .formatMessage(
+      JvOptionPane.showMessageDialog(Desktop.desktop,
+              MessageManager.formatMessage(
                       "label.secondary_structure_prediction_service_couldnt_be_located",
-                      new String[] { WebServiceName, WsURL })
-              + "\n" + ex.getMessage());
+                      new String[]
+                      { WebServiceName, WsURL }),
+              MessageManager.getString("label.internal_jalview_error"),
+              JvOptionPane.WARNING_MESSAGE);
+      wsInfo.setProgressText(MessageManager.formatMessage(
+              "label.secondary_structure_prediction_service_couldnt_be_located",
+              new String[]
+              { WebServiceName, WsURL }) + "\n" + ex.getMessage());
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
 
     }
@@ -360,8 +358,8 @@ public class JPredClient extends WS1Client
         if (msa.getSequences().length == 1)
         {
           // Single Sequence prediction
-          new jalview.ws.jws1.JPredClient(sh, af.getTitle(), false, msa,
-                  af, true);
+          new jalview.ws.jws1.JPredClient(sh, af.getTitle(), false, msa, af,
+                  true);
         }
         else
         {