JAL-4059 Tidy getting the namespace, and save the namespace in the Jalview instance...

[jalview.git] / src / jalview / gui / StructureChooser.java

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 8135019..21b380d 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -78,6 +78,8 @@ import jalview.jbgui.GStructureChooser;
 import jalview.structure.StructureImportSettings.TFType;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.StringUtils;
@@ -139,8 +141,10 @@ public class StructureChooser extends GStructureChooser
   List<SequenceI> seqsWithoutSourceDBRef = null;
 
   private boolean showChooserGUI = true;
+
   /**
-   * when true, queries to external services are supressed (no SIFTs, no PDBe, no 3D-Beacons, etc)
+   * when true, queries to external services are supressed (no SIFTs, no PDBe,
+   * no 3D-Beacons, etc)
    */
   private boolean dontQueryServices = false;
 
@@ -157,7 +161,7 @@ public class StructureChooser extends GStructureChooser
   {
     this(selectedSeqs, selectedSeq, ap, showGUI, false);
   }
-  
+
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap, boolean showGUI, boolean dontQueryServices)
   {
@@ -255,8 +259,11 @@ public class StructureChooser extends GStructureChooser
         }
 
       }).start();
-    } else {
-      Console.debug("Structure chooser not querying services to discover metadata.");
+    }
+    else
+    {
+      Console.debug(
+              "Structure chooser not querying services to discover metadata.");
     }
   }
 
@@ -303,7 +310,7 @@ public class StructureChooser extends GStructureChooser
    */
   public void promptForTDBFetch(boolean ignoreGui)
   {
-    final long progressId = System.currentTimeMillis();
+    final long progressId = IdUtils.newId(IdType.PROGRESS);
 
     // final action after prompting and discovering db refs
     final Runnable strucDiscovery = new Runnable()
@@ -1008,10 +1015,11 @@ public class StructureChooser extends GStructureChooser
               .getFTSDataFor(getResultTable(), selectedRow,
                       discoveredStructuresSet);
       String pageUrl = row.getModelViewUrl();
-      
+
       JPopupMenu popup = new JPopupMenu("3D Beacons");
       JMenuItem viewUrl = new JMenuItem("View model web page");
-      if (pageUrl == null || "".equals(pageUrl.trim())) {
+      if (pageUrl == null || "".equals(pageUrl.trim()))
+      {
         viewUrl.setEnabled(false);
         viewUrl.setText("No model page available.");
       }
@@ -1243,7 +1251,7 @@ public class StructureChooser extends GStructureChooser
 
     final String progress = MessageManager
             .getString("label.working_ellipsis");
-    setProgressBar(progress, progress.hashCode());
+    setProgressBar(progress, IdUtils.newId(IdType.PROGRESS, progress));
     Runnable viewStruc = new Runnable()
     {
       @Override
@@ -1348,7 +1356,8 @@ public class StructureChooser extends GStructureChooser
           @Override
           public void run()
           {
-            setProgressBar("Complete.", progress.hashCode());
+            setProgressBar("Complete.",
+                    IdUtils.newId(IdType.PROGRESS, progress));
             closeAction(preferredHeight);
             mainFrame.dispose();
           }
@@ -1814,7 +1823,8 @@ public class StructureChooser extends GStructureChooser
       // headless = true;
       prompt = false;
       // suppress structure viewer's external service queries
-      sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false,true);
+      sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false,
+              true);
     }
     if (ssm == null)
     {