JAL-1620 version bump and release notes

[jalview.git] / src / jalview / ws / DasSequenceFeatureFetcher.java

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index ff715ba..d8d2db4 100644 (file)
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -27,6 +27,7 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.FeatureSettings;
+import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
@@ -204,9 +205,8 @@ public class DasSequenceFeatureFetcher
         reply = JOptionPane
                 .showInternalConfirmDialog(
                         Desktop.desktop,
-                        "Do you want Jalview to find\n"
-                                + "Uniprot Accession ids for given sequence names?",
-                        "Find Uniprot Accession Ids",
+                        MessageManager.getString("info.you_want_jalview_to_find_uniprot_accessions"),
+                        MessageManager.getString("label.find_uniprot_accession_ids"),
                         JOptionPane.YES_NO_OPTION,
                         JOptionPane.QUESTION_MESSAGE);
       }
@@ -264,7 +264,7 @@ public class DasSequenceFeatureFetcher
     startTime = System.currentTimeMillis();
     if (af != null)
     {
-      af.setProgressBar("Fetching DAS Sequence Features", startTime);
+      af.setProgressBar(MessageManager.getString("status.fetching_das_sequence_features"), startTime);
     }
     if (sourceRegistry == null)
     {
@@ -496,13 +496,13 @@ public class DasSequenceFeatureFetcher
                 } catch (Exception ex)
                 {
                   Cache.log
-                          .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");
-                  Cache.log.info("Mapping feature from " + f.getBegin()
+                          .warn("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");
+                  Cache.log.warn("Mapping feature from " + f.getBegin()
                           + " to " + f.getEnd() + " in dbref "
                           + dbref.getAccessionId() + " in "
                           + dbref.getSource());
-                  Cache.log.info("using das Source " + source);
-                  Cache.log.info("Exception", ex);
+                  Cache.log.warn("using das Source " + source);
+                  Cache.log.warn("Exception", ex);
                 }
 
                 if (vf != null)
@@ -537,7 +537,7 @@ public class DasSequenceFeatureFetcher
 
     if (af != null)
     {
-      af.setProgressBar("No DAS Sources Active", startTime);
+      af.setProgressBar(MessageManager.getString("status.no_das_sources_active"), startTime);
     }
     if (getFeatSettings() != null)
     {
@@ -567,7 +567,7 @@ public class DasSequenceFeatureFetcher
   {
     if (af != null)
     {
-      af.setProgressBar("DAS Feature Fetching Cancelled", startTime);
+      af.setProgressBar(MessageManager.getString("status.das_feature_fetching_cancelled"), startTime);
     }
     cancelled = true;
   }
@@ -582,7 +582,7 @@ public class DasSequenceFeatureFetcher
     if (!cancelled && af != null)
     {
       // only update the progress bar if we've completed the fetch normally
-      af.setProgressBar("DAS Feature Fetching Complete", startTime);
+      af.setProgressBar(MessageManager.getString("status.das_feature_fetching_complete"), startTime);
     }
 
     if (af != null && af.featureSettings != null)
@@ -626,7 +626,9 @@ public class DasSequenceFeatureFetcher
   Object[] nextSequence(jalviewSourceI dasSource, SequenceI seq)
   {
     if (cancelled)
+    {
       return null;
+    }
     DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
             seq.getDBRef(), new String[]
             {
@@ -668,7 +670,9 @@ public class DasSequenceFeatureFetcher
             qstring.add(uprefs[j].getAccessionId());
           }
           else
+          {
             System.out.println("IGNORE " + csys.getAuthority());
+          }
         }
       }
     }
@@ -839,7 +843,7 @@ public class DasSequenceFeatureFetcher
       {
         for (String note : feat.getNOTE())
         {
-          desc += (String) note;
+          desc += note;
         }
       }