From 94ca0419cc7afa75b3c51917a8beaf46a7c05540 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Fri, 3 Nov 2023 15:37:07 +0000
Subject: [PATCH] JAL-4239 Using own id generation to avoid Random.nextLong()
 not implemented in jalviewjs

---
 src/jalview/bin/Commands.java                      |   18 ++--
 src/jalview/bin/Jalview.java                       |    6 +-
 src/jalview/gui/AnnotationLabels.java              |   37 +++++---
 src/jalview/gui/CrossRefAction.java                |   23 ++---
 src/jalview/gui/Desktop.java                       |   67 ++++++++------
 src/jalview/gui/PCAPanel.java                      |   14 ++-
 src/jalview/gui/SequenceFetcher.java               |   11 ++-
 src/jalview/gui/StructureChooser.java              |   30 ++++---
 src/jalview/gui/StructureViewerBase.java           |   78 +++++++++-------
 src/jalview/gui/WsPreferences.java                 |    4 +-
 src/jalview/io/HTMLOutput.java                     |    7 +-
 .../structure/StructureSelectionManager.java       |   35 +++++---
 src/jalview/util/IdUtils.java                      |   95 ++++++++++++++++++++
 src/jalview/ws/DBRefFetcher.java                   |   22 ++---
 src/jalview/ws/jws2/AbstractJabaCalcWorker.java    |   38 ++++----
 src/jalview/ws/jws2/MsaWSThread.java               |   31 +++----
 16 files changed, 357 insertions(+), 159 deletions(-)
 create mode 100644 src/jalview/util/IdUtils.java

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index a092cd6..e4e0e59 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -55,6 +55,8 @@ import jalview.structure.StructureSelectionManager;
 import jalview.util.ColorUtils;
 import jalview.util.FileUtils;
 import jalview.util.HttpUtils;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.ImageMaker;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
@@ -225,7 +227,7 @@ public class Commands
             desktop.setProgressBar(
                     MessageManager.getString(
                             "status.processing_commandline_args"),
-                    progress = System.currentTimeMillis());
+                    progress = IdUtils.newId(IdType.PROGRESS));
             progressBarSet = true;
           }
         }
@@ -363,21 +365,22 @@ public class Commands
             }
           }
 
-          
           // Show secondary structure annotations?
           boolean showSSAnnotations = avm.getFromSubValArgOrPref(
                   Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
                   "STRUCT_FROM_PDB", true);
-          
+
           // Show sequence annotations?
           boolean showAnnotations = avm.getFromSubValArgOrPref(
                   Arg.SHOWANNOTATIONS, av.getSubVals(), null,
                   "SHOW_ANNOTATIONS", true);
-          
+
           boolean hideTFrows = (avm.getBoolean(Arg.NOTEMPFAC));
           final AlignFrame _af = af;
-          // many of jalview's format/layout methods are only thread safe on the swingworker thread.
-          // all these methods should be on the alignViewController so it can coordinate such details
+          // many of jalview's format/layout methods are only thread safe on the
+          // swingworker thread.
+          // all these methods should be on the alignViewController so it can
+          // coordinate such details
           try
           {
             SwingUtilities.invokeAndWait(new Runnable()
@@ -457,8 +460,9 @@ public class Commands
         }
       }
       if (progressBarSet && desktop != null)
+      {
         desktop.setProgressBar(null, progress);
-
+      }
     }
 
     // open the structure (from same PDB file or given PDBfile)
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 3ffcdd0..ba9c5b0 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -100,6 +100,8 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.ChannelProperties;
 import jalview.util.HttpUtils;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.LaunchUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -206,7 +208,7 @@ public class Jalview implements JalviewObjectI
     public void addFetcher(final AlignFrame af,
             final Vector<String> dasSources)
     {
-      final long id = System.currentTimeMillis();
+      final long id = IdUtils.newId(IdType.PROGRESS);
       queued++;
       final FeatureFetcher us = this;
       new Thread(new Runnable()
@@ -911,7 +913,7 @@ public class Jalview implements JalviewObjectI
         desktop.setProgressBar(
                 MessageManager
                         .getString("status.processing_commandline_args"),
-                progress = System.currentTimeMillis());
+                progress = IdUtils.newId(IdType.PROGRESS));
       }
       Console.outPrintln("CMD [-open " + file + "] executed successfully!");
 
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 08a25ba..1c1602c 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -65,6 +65,8 @@ import jalview.datamodel.SequenceI;
 import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.util.Comparison;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 
@@ -565,7 +567,7 @@ public class AnnotationLabels extends JPanel
                         MessageManager.formatMessage(
                                 "action.clustering_matrix_for",
                                 cm.getAnnotDescr(), 5f),
-                        progBar = System.currentTimeMillis());
+                        progBar = IdUtils.newId(IdType.PROGRESS));
                 cm.setGroupSet(GroupSet.makeGroups(cm, true));
                 cm.randomlyReColourGroups();
                 cm.transferGroupColorsTo(alignmentAnnotation);
@@ -1198,7 +1200,8 @@ public class AnnotationLabels extends JPanel
    * @param width
    *          Width for scaling labels
    */
-  public void drawComponent(Graphics g, boolean clip, int givenWidth, boolean forGUI)
+  public void drawComponent(Graphics g, boolean clip, int givenWidth,
+          boolean forGUI)
   {
     int width = givenWidth;
     IdwidthAdjuster iwa = null;
@@ -1210,8 +1213,8 @@ public class AnnotationLabels extends JPanel
       {
         Graphics2D g2d = (Graphics2D) g;
         Graphics dummy = g2d.create();
-        int newAnnotationIdWidth = drawLabels(dummy, clip, width, false, forGUI,
-                null, false);
+        int newAnnotationIdWidth = drawLabels(dummy, clip, width, false,
+                forGUI, null, false);
         dummy.dispose();
         Dimension d = ap.calculateDefaultAlignmentIdWidth();
         int alignmentIdWidth = d.width;
@@ -1245,8 +1248,10 @@ public class AnnotationLabels extends JPanel
     }
     else
     {
-      int newAnnotationIdWidth = drawLabels(g, clip, width, false, forGUI, null, false);
-      width = newAnnotationIdWidth<givenWidth ? givenWidth: Math.min(newAnnotationIdWidth, givenWidth);
+      int newAnnotationIdWidth = drawLabels(g, clip, width, false, forGUI,
+              null, false);
+      width = newAnnotationIdWidth < givenWidth ? givenWidth
+              : Math.min(newAnnotationIdWidth, givenWidth);
     }
     drawLabels(g, clip, width, true, forGUI, null, false);
   }
@@ -1258,21 +1263,28 @@ public class AnnotationLabels extends JPanel
    * fmetrics must be supplied.
    * 
    * @param g
-   *          Graphics2D instance (used for rendering and font scaling if no fmetrics supplied) 
+   *          Graphics2D instance (used for rendering and font scaling if no
+   *          fmetrics supplied)
    * @param clip
    *          - true indicates that only current visible area needs to be
    *          rendered
    * @param width
    *          Width for scaling labels
-   * @param actuallyDraw - when false, no graphics are rendered to g0
-   * @param forGUI - when false, GUI relevant marks like indicators for dragging annotation panel height are not rendered
+   * @param actuallyDraw
+   *          - when false, no graphics are rendered to g0
+   * @param forGUI
+   *          - when false, GUI relevant marks like indicators for dragging
+   *          annotation panel height are not rendered
    * @param fmetrics
    *          FontMetrics if Graphics object g is null
-   * @param includeHidden - when true returned width includes labels in hidden row width calculation 
+   * @param includeHidden
+   *          - when true returned width includes labels in hidden row width
+   *          calculation
    * @return the width of the annotation labels.
    */
   public int drawLabels(Graphics g0, boolean clip, int width,
-          boolean actuallyDraw, boolean forGUI, FontMetrics fmetrics, boolean includeHidden)
+          boolean actuallyDraw, boolean forGUI, FontMetrics fmetrics,
+          boolean includeHidden)
   {
     if (clip)
     {
@@ -1554,7 +1566,8 @@ public class AnnotationLabels extends JPanel
       }
     }
 
-    if (!resizePanel && dragEvent != null && aa != null && selectedRow>-1 && selectedRow<aa.length)
+    if (!resizePanel && dragEvent != null && aa != null && selectedRow > -1
+            && selectedRow < aa.length)
     {
       if (actuallyDraw && g != null)
       {
diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 6cb59c3..9580ef8 100644
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -20,6 +20,12 @@
  */
 package jalview.gui;
 
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.CrossRef;
 import jalview.api.AlignmentViewPanel;
@@ -37,18 +43,14 @@ import jalview.ext.ensembl.EnsemblMap;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.DBRefUtils;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 import jalview.ws.SequenceFetcher;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
 /**
  * Factory constructor and runnable for discovering and displaying
  * cross-references for a set of aligned sequences
@@ -76,10 +78,10 @@ public class CrossRefAction implements Runnable
   @Override
   public void run()
   {
-    final long sttime = System.currentTimeMillis();
+    final long id = IdUtils.newId(IdType.PROGRESS);
     alignFrame.setProgressBar(MessageManager.formatMessage(
             "status.searching_for_sequences_from", new Object[]
-            { source }), sttime);
+            { source }), id);
     try
     {
       AlignmentI alignment = alignFrame.getViewport().getAlignment();
@@ -237,7 +239,7 @@ public class CrossRefAction implements Runnable
     {
       alignFrame.setProgressBar(MessageManager.formatMessage(
               "status.finished_searching_for_sequences_from", new Object[]
-              { source }), sttime);
+              { source }), id);
     }
   }
 
@@ -466,7 +468,8 @@ public class CrossRefAction implements Runnable
 
     if (copyAlignment.getHeight() <= 0)
     {
-      jalview.bin.Console.errPrintln("No Sequences generated for xRef type " + source);
+      jalview.bin.Console
+              .errPrintln("No Sequences generated for xRef type " + source);
       return null;
     }
 
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 070e67d..85cfc1c 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -141,6 +141,8 @@ import jalview.structure.StructureSelectionManager;
 import jalview.urls.IdOrgSettings;
 import jalview.util.BrowserLauncher;
 import jalview.util.ChannelProperties;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.LaunchUtils;
 import jalview.util.MessageManager;
@@ -759,11 +761,12 @@ public class Desktop extends jalview.jbgui.GDesktop
         @Override
         public void run()
         {
-          long now = System.currentTimeMillis();
+          long progressId = IdUtils.newId(IdType.PROGRESS);
           Desktop.instance.setProgressBar(
-                  MessageManager.getString("status.refreshing_news"), now);
+                  MessageManager.getString("status.refreshing_news"),
+                  progressId);
           jvnews.refreshNews();
-          Desktop.instance.setProgressBar(null, now);
+          Desktop.instance.setProgressBar(null, progressId);
           jvnews.showNews();
         }
       }).start();
@@ -1478,16 +1481,21 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   /**
-   * close everything, stash window geometries, and shut down all associated threads/workers  
-   * @param dispose - sets the dispose on close flag - JVM may terminate when set
-   * @param terminateJvm - quit with prejudice - stops the JVM.
+   * close everything, stash window geometries, and shut down all associated
+   * threads/workers
+   * 
+   * @param dispose
+   *          - sets the dispose on close flag - JVM may terminate when set
+   * @param terminateJvm
+   *          - quit with prejudice - stops the JVM.
    */
-  public void quitTheDesktop(boolean dispose, boolean terminateJvm) {
+  public void quitTheDesktop(boolean dispose, boolean terminateJvm)
+  {
     Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
     Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
     Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + "");
-    storeLastKnownDimensions("", new Rectangle(getBounds().x,
-            getBounds().y, getWidth(), getHeight()));
+    storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
+            getWidth(), getHeight()));
 
     if (jconsole != null)
     {
@@ -1530,19 +1538,22 @@ public class Desktop extends jalview.jbgui.GDesktop
       // instance.dispose();
     }
   }
+
   public QuitHandler.QResponse desktopQuit(boolean ui, boolean disposeFlag)
   {
     final Runnable doDesktopQuit = () -> {
 
-      // FIRST !!  check for aborted quit
+      // FIRST !! check for aborted quit
       if (QuitHandler.quitCancelled())
       {
-        jalview.bin.Console.debug("Quit was cancelled - Desktop aborting quit");
+        jalview.bin.Console
+                .debug("Quit was cancelled - Desktop aborting quit");
         return;
       }
-      
+
       // Proceed with quitting
-      quitTheDesktop(disposeFlag, QuitHandler.gotQuitResponse() == QResponse.FORCE_QUIT);
+      quitTheDesktop(disposeFlag,
+              QuitHandler.gotQuitResponse() == QResponse.FORCE_QUIT);
       // and exit the JVM
       instance.quit();
     };
@@ -1552,13 +1563,13 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   /**
-   * Exits the program and the JVM. 
+   * Exits the program and the JVM.
    * 
    * Don't call this directly
    * 
    * - use desktopQuit() above to tidy up first.
    * 
-   * - use closeDesktop() to shutdown Jalview without shutting down the JVM 
+   * - use closeDesktop() to shutdown Jalview without shutting down the JVM
    * 
    */
   @Override
@@ -1948,7 +1959,8 @@ public class Desktop extends jalview.jbgui.GDesktop
           // TODO: refactor to Jalview desktop session controller action.
           setProgressBar(MessageManager.formatMessage(
                   "label.saving_jalview_project", new Object[]
-                  { chosenFile.getName() }), chosenFile.hashCode());
+                  { chosenFile.getName() }),
+                  IdUtils.newId(IdType.PROGRESS, chosenFile));
           Cache.setProperty("LAST_DIRECTORY", chosenFile.getParent());
           // TODO catch and handle errors for savestate
           // TODO prevent user from messing with the Desktop whilst we're saving
@@ -1982,7 +1994,7 @@ public class Desktop extends jalview.jbgui.GDesktop
                     MessageManager.getString("label.couldnt_save_project"),
                     JvOptionPane.WARNING_MESSAGE);
           }
-          setProgressBar(null, chosenFile.hashCode());
+          setProgressBar(null, IdUtils.newId(IdType.PROGRESS, chosenFile));
         }
       }).start();
     }
@@ -3067,13 +3079,16 @@ public class Desktop extends jalview.jbgui.GDesktop
    */
   public static void showUrl(final String url)
   {
-    if (url!=null && !url.trim().equals("")) {
-      jalview.bin.Console.info("Opening URL: "+url);
+    if (url != null && !url.trim().equals(""))
+    {
+      jalview.bin.Console.info("Opening URL: " + url);
       showUrl(url, Desktop.instance);
-    } else {
+    }
+    else
+    {
       jalview.bin.Console.warn("Ignoring attempt to show an empty URL.");
     }
-    
+
   }
 
   /**
@@ -3097,7 +3112,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           {
             progress.setProgressBar(MessageManager
                     .formatMessage("status.opening_params", new Object[]
-                    { url }), this.hashCode());
+                    { url }), IdUtils.newId(IdType.PROGRESS, this));
           }
           jalview.util.BrowserLauncher.openURL(url);
         } catch (Exception ex)
@@ -3112,7 +3127,8 @@ public class Desktop extends jalview.jbgui.GDesktop
         }
         if (progress != null)
         {
-          progress.setProgressBar(null, this.hashCode());
+          progress.setProgressBar(null,
+                  IdUtils.newId(IdType.PROGRESS, this));
         }
       }
     }).start();
@@ -3724,8 +3740,9 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   /**
-   * closes the current instance window, but leaves the JVM running.
-   * Bypasses any shutdown prompts, but does not set window dispose on close in case JVM terminates.
+   * closes the current instance window, but leaves the JVM running. Bypasses
+   * any shutdown prompts, but does not set window dispose on close in case JVM
+   * terminates.
    */
   public static void closeDesktop()
   {
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 211c370..44a65ba 100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -52,6 +52,8 @@ import jalview.gui.JalviewColourChooser.ColourChooserListener;
 import jalview.io.exceptions.ImageOutputException;
 import jalview.jbgui.GPCAPanel;
 import jalview.math.RotatableMatrix.Axis;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
@@ -174,7 +176,7 @@ public class PCAPanel extends GPCAPanel
   public void run()
   {
     working = true;
-    long progId = System.currentTimeMillis();
+    long progId = IdUtils.newId(IdType.PROGRESS);
     IProgressIndicator progress = this;
     String message = MessageManager.getString("label.pca_recalculating");
     if (getParent() == null)
@@ -419,6 +421,7 @@ public class PCAPanel extends GPCAPanel
     }
   }
 
+  @Override
   public void makePCAImage(ImageMaker.TYPE type)
   {
     int width = getRotatableCanvas().getWidth();
@@ -439,10 +442,13 @@ public class PCAPanel extends GPCAPanel
     };
     String pca = MessageManager.getString("label.pca");
     ImageExporter exporter = new ImageExporter(writer, null, type, pca);
-    try {
+    try
+    {
       exporter.doExport(null, this, width, height, pca);
-    } catch (ImageOutputException ioex) {
-      Console.error("Unexpected error whilst writing "+type.toString(),ioex);
+    } catch (ImageOutputException ioex)
+    {
+      Console.error("Unexpected error whilst writing " + type.toString(),
+              ioex);
     }
   }
 
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 137655f..77bac76 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -55,6 +55,8 @@ import jalview.fts.service.uniprot.UniprotFTSPanel;
 import jalview.io.FileFormatI;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.util.DBRefUtils;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.seqfetcher.DbSourceProxy;
@@ -571,7 +573,7 @@ public class SequenceFetcher extends JPanel implements Runnable
                 "status.fetching_sequence_queries_from", new String[]
                 { Integer.valueOf(nqueries).toString(),
                     proxy.getDbName() }),
-                Thread.currentThread().hashCode());
+                IdUtils.newId(IdType.PROGRESS, Thread.currentThread()));
         if (proxy.getMaximumQueryCount() == 1)
         {
           /*
@@ -667,7 +669,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       }
       guiWindow.setProgressBar(
               MessageManager.getString("status.finshed_querying"),
-              Thread.currentThread().hashCode());
+              IdUtils.newId(IdType.PROGRESS, Thread.currentThread()));
     }
     guiWindow
             .setProgressBar(
@@ -675,7 +677,7 @@ public class SequenceFetcher extends JPanel implements Runnable
                             ? MessageManager
                                     .getString("status.parsing_results")
                             : MessageManager.getString("status.processing"),
-                    Thread.currentThread().hashCode());
+                    IdUtils.newId(IdType.PROGRESS, Thread.currentThread()));
     // process results
     while (presult.size() > 0)
     {
@@ -683,7 +685,8 @@ public class SequenceFetcher extends JPanel implements Runnable
               preferredFeatureColours);
     }
     // only remove visual delay after we finished parsing.
-    guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
+    guiWindow.setProgressBar(null,
+            IdUtils.newId(IdType.PROGRESS, Thread.currentThread()));
     if (nextFetch.size() > 0)
     {
       StringBuffer sb = new StringBuffer();
diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 8135019..21b380d 100644
--- 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)
     {
diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 085be71..1f39b54 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -66,6 +66,8 @@ import jalview.schemes.ColourSchemes;
 import jalview.structure.StructureMapping;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.BrowserLauncher;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.MessageManager;
 import jalview.ws.dbsources.EBIAlfaFold;
 import jalview.ws.dbsources.Pdb;
@@ -90,8 +92,9 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   /**
-   * Singleton list of all (open) instances of structureViewerBase
-   * TODO: JAL-3362 - review and adopt the swingJS-safe singleton pattern so each structure viewer base instance is kept to its own JalviewJS parent
+   * Singleton list of all (open) instances of structureViewerBase TODO:
+   * JAL-3362 - review and adopt the swingJS-safe singleton pattern so each
+   * structure viewer base instance is kept to its own JalviewJS parent
    */
   private static List<JalviewStructureDisplayI> svbs = new ArrayList<>();
 
@@ -225,11 +228,13 @@ public abstract class StructureViewerBase extends GStructureViewer
    * 
    * @return TRUE if the view is NOT being coloured by the alignment colours.
    */
+  @Override
   public boolean isColouredByViewer()
   {
     return !getBinding().isColourBySequence();
   }
 
+  @Override
   public String getViewId()
   {
     if (viewId == null)
@@ -392,6 +397,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
   }
 
+  @Override
   public abstract ViewerType getViewerType();
 
   /**
@@ -607,7 +613,8 @@ public abstract class StructureViewerBase extends GStructureViewer
       chainMenu.add(menuItem);
     }
   }
-  void setHetatmMenuItems(Map<String,String> hetatmNames)
+
+  void setHetatmMenuItems(Map<String, String> hetatmNames)
   {
     hetatmMenu.removeAll();
     if (hetatmNames == null || hetatmNames.isEmpty())
@@ -616,7 +623,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       return;
     }
     hetatmMenu.setVisible(true);
-    allHetatmBeingSelected=false;
+    allHetatmBeingSelected = false;
     JMenuItem allMenuItem = new JMenuItem(
             MessageManager.getString("label.all"));
     JMenuItem noneMenuItem = new JMenuItem(
@@ -624,46 +631,52 @@ public abstract class StructureViewerBase extends GStructureViewer
     allMenuItem.addActionListener(new ActionListener()
     {
       @Override
-      public void actionPerformed(ActionEvent e) {
+      public void actionPerformed(ActionEvent e)
       {
-        allHetatmBeingSelected=true;
-        // Toggle state of everything - on
-        for (int i = 0; i < hetatmMenu.getItemCount(); i++)
         {
-          if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+          allHetatmBeingSelected = true;
+          // Toggle state of everything - on
+          for (int i = 0; i < hetatmMenu.getItemCount(); i++)
           {
-            ((JCheckBoxMenuItem) hetatmMenu.getItem(i)).setSelected(true);
+            if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+            {
+              ((JCheckBoxMenuItem) hetatmMenu.getItem(i)).setSelected(true);
+            }
           }
+          allHetatmBeingSelected = false;
+          showSelectedHetatms();
         }
-        allHetatmBeingSelected=false;
-        showSelectedHetatms();
       }
-      }});
+    });
 
     noneMenuItem.addActionListener(new ActionListener()
     {
       @Override
-      public void actionPerformed(ActionEvent e) {
+      public void actionPerformed(ActionEvent e)
       {
-        allHetatmBeingSelected=true;
-        // Toggle state of everything off
-        for (int i = 0; i < hetatmMenu.getItemCount(); i++)
         {
-          if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+          allHetatmBeingSelected = true;
+          // Toggle state of everything off
+          for (int i = 0; i < hetatmMenu.getItemCount(); i++)
           {
-            ((JCheckBoxMenuItem) hetatmMenu.getItem(i)).setSelected(false);
+            if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+            {
+              ((JCheckBoxMenuItem) hetatmMenu.getItem(i))
+                      .setSelected(false);
+            }
           }
+          allHetatmBeingSelected = false;
+          showSelectedHetatms();
         }
-        allHetatmBeingSelected=false;
-        showSelectedHetatms();
       }
-      }});
+    });
     hetatmMenu.add(noneMenuItem);
     hetatmMenu.add(allMenuItem);
 
     for (Map.Entry<String, String> chain : hetatmNames.entrySet())
     {
-      JCheckBoxMenuItem menuItem = new JCheckBoxMenuItem(chain.getKey(), false);
+      JCheckBoxMenuItem menuItem = new JCheckBoxMenuItem(chain.getKey(),
+              false);
       menuItem.setToolTipText(chain.getValue());
       menuItem.addItemListener(new ItemListener()
       {
@@ -671,7 +684,7 @@ public abstract class StructureViewerBase extends GStructureViewer
         public void itemStateChanged(ItemEvent evt)
         {
           if (!allHetatmBeingSelected)
-          { 
+          {
             // update viewer only when we were clicked, not programmatically
             // checked/unchecked
             showSelectedHetatms();
@@ -1177,7 +1190,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   {
     // TODO would rather have startProgress/stopProgress as the
     // IProgressIndicator interface
-    long tm = random.nextLong();
+    long tm = IdUtils.newId(IdType.PROGRESS);
     if (progressBar != null)
     {
       progressBar.setProgressBar(msg, tm);
@@ -1237,6 +1250,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
     getBinding().showChains(toshow);
   }
+
   /**
    * Display selected hetatms in viewer
    */
@@ -1256,6 +1270,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
     getBinding().showHetatms(toshow);
   }
+
   /**
    * Tries to fetch a PDB file and save to a temporary local file. Returns the
    * saved file path if successful, or null if not.
@@ -1270,8 +1285,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     EBIAlfaFold afclient = new EBIAlfaFold();
     AlignmentI pdbseq = null;
     String pdbid = processingEntry.getId();
-    long handle = System.currentTimeMillis()
-            + Thread.currentThread().hashCode();
+    long handle = IdUtils.newId(IdType.PROGRESS);
 
     /*
      * Write 'fetching PDB' progress on AlignFrame as we are not yet visible
@@ -1348,6 +1362,7 @@ public abstract class StructureViewerBase extends GStructureViewer
    * 
    * @return
    */
+  @Override
   public File saveSession()
   {
     if (getBinding() == null)
@@ -1459,12 +1474,15 @@ public abstract class StructureViewerBase extends GStructureViewer
     // TODO: check for memory leaks where instance isn't finalised because jmb
     // holds a reference to the window
     // jmb = null;
-    
-    try {
+
+    try
+    {
       svbs.remove(this);
     } catch (Throwable t)
     {
-      Console.info("Unexpected exception when deregistering structure viewer",t);
+      Console.info(
+              "Unexpected exception when deregistering structure viewer",
+              t);
     }
     dispose();
   }
diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java
index e37f77c..ea3dd0d 100644
--- a/src/jalview/gui/WsPreferences.java
+++ b/src/jalview/gui/WsPreferences.java
@@ -39,6 +39,8 @@ import javax.swing.table.TableCellRenderer;
 
 import jalview.bin.Cache;
 import jalview.jbgui.GWsPreferences;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.MessageManager;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.rest.RestServiceDescription;
@@ -614,7 +616,7 @@ public class WsPreferences extends GWsPreferences
         @Override
         public void run()
         {
-          long ct = System.currentTimeMillis();
+          long ct = IdUtils.newId(IdType.PROGRESS);
           Desktop.instance.setProgressBar(MessageManager
                   .getString("status.refreshing_web_service_menus"), ct);
           if (lastrefresh != update)
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 02d46e7..711c465 100644
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -35,6 +35,8 @@ import jalview.datamodel.AlignmentExportData;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.IProgressIndicator;
 import jalview.io.exceptions.ImageOutputException;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.MessageManager;
 
 public abstract class HTMLOutput implements Runnable
@@ -68,7 +70,7 @@ public abstract class HTMLOutput implements Runnable
     this.ap = ap;
     this.pIndicator = ap.alignFrame;
     this.description = desc;
-    this.pSessionId = System.currentTimeMillis();
+    this.pSessionId = IdUtils.newId(IdType.PROGRESS);
   }
 
   /**
@@ -308,7 +310,8 @@ public abstract class HTMLOutput implements Runnable
     exportHTML(outputFile, null);
   }
 
-  public void exportHTML(String outputFile, String renderer) throws ImageOutputException
+  public void exportHTML(String outputFile, String renderer)
+          throws ImageOutputException
   {
     setProgressMessage(MessageManager.formatMessage(
             "status.exporting_alignment_as_x_file", getDescription()));
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 2f1ddc0..0356828 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -54,6 +54,8 @@ import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.structure.StructureImportSettings.TFType;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -155,7 +157,8 @@ public class StructureSelectionManager
   {
     if (mappings.isEmpty())
     {
-      jalview.bin.Console.errPrintln("reportMapping: No PDB/Sequence mappings.");
+      jalview.bin.Console
+              .errPrintln("reportMapping: No PDB/Sequence mappings.");
     }
     else
     {
@@ -164,7 +167,8 @@ public class StructureSelectionManager
       int i = 0;
       for (StructureMapping sm : mappings)
       {
-        jalview.bin.Console.errPrintln("mapping " + i++ + " : " + sm.pdbfile);
+        jalview.bin.Console
+                .errPrintln("mapping " + i++ + " : " + sm.pdbfile);
       }
     }
   }
@@ -357,7 +361,6 @@ public class StructureSelectionManager
             pdbFile, sourceType, tft, paeFilename, true);
   }
 
-
   /**
    * create sequence structure mappings between each sequence and the given
    * pdbFile (retrieved via the given protocol). Either constructs a mapping
@@ -377,9 +380,15 @@ public class StructureSelectionManager
    *          - structure data resource
    * @param sourceType
    *          - how to resolve data from resource
-   * @param tft - specify how to interpret the temperature factor column in the atom data
-   * @param paeFilename - when not null, specifies a filename containing a matrix formatted in JSON using one of the known PAE formats
-   * @param doXferSettings - when true, transfer annotation to mapped sequences in sequenceArray 
+   * @param tft
+   *          - specify how to interpret the temperature factor column in the
+   *          atom data
+   * @param paeFilename
+   *          - when not null, specifies a filename containing a matrix
+   *          formatted in JSON using one of the known PAE formats
+   * @param doXferSettings
+   *          - when true, transfer annotation to mapped sequences in
+   *          sequenceArray
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public StructureFile setMapping(boolean forStructureView,
@@ -413,9 +422,15 @@ public class StructureSelectionManager
    * @param IProgressIndicator
    *          reference to UI component that maintains a progress bar for the
    *          mapping operation
-   * @param tft - specify how to interpret the temperature factor column in the atom data
-   * @param paeFilename - when not null, specifies a filename containing a matrix formatted in JSON using one of the known PAE formats
-   * @param doXferSettings - when true, transfer annotation to mapped sequences in sequenceArray 
+   * @param tft
+   *          - specify how to interpret the temperature factor column in the
+   *          atom data
+   * @param paeFilename
+   *          - when not null, specifies a filename containing a matrix
+   *          formatted in JSON using one of the known PAE formats
+   * @param doXferSettings
+   *          - when true, transfer annotation to mapped sequences in
+   *          sequenceArray
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public StructureFile computeMapping(boolean forStructureView,
@@ -424,7 +439,7 @@ public class StructureSelectionManager
           IProgressIndicator progress, TFType tft, String paeFilename,
           boolean doXferSettings)
   {
-    long progressSessionId = System.currentTimeMillis() * 3;
+    long progressSessionId = IdUtils.newId(IdType.PROGRESS);
 
     /**
      * do we extract and transfer annotation from 3D data ?
diff --git a/src/jalview/util/IdUtils.java b/src/jalview/util/IdUtils.java
new file mode 100644
index 0000000..38ea260
--- /dev/null
+++ b/src/jalview/util/IdUtils.java
@@ -0,0 +1,95 @@
+package jalview.util;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import jalview.bin.Console;
+
+public class IdUtils
+{
+  /**
+   * id generating tools avoiding Random.nextLong() for JalviewJS. Avoids
+   * collisions.
+   */
+
+  public static enum IdType
+  {
+    GENERAL, PROGRESS;
+  }
+
+  private static int count = 0;
+
+  private static Map<IdType, Set<Long>> typeMap = new HashMap<>();
+
+  static
+  {
+    for (IdType t : IdType.values())
+    {
+      typeMap.put(t, new HashSet<>());
+    }
+  }
+
+  public static long newId()
+  {
+    return newId(IdType.GENERAL, null);
+  }
+
+  public static long newId(IdType t)
+  {
+    return newId(t, null);
+  }
+
+  public static long newId(IdType t, Object o)
+  {
+    Set<Long> idSet = typeMap.get(t);
+    long newId = 0;
+    if (o == null)
+    {
+      // get a new hashCode -- not tied to an object.
+      // Adding Integer.MAX_VALUE should avoid collisions with object generated
+      // Ids.
+      newId = Integer.MAX_VALUE + t.hashCode() + System.currentTimeMillis()
+              + count;
+      while (idSet.contains(newId))
+      {
+        newId += count;
+      }
+    }
+    else
+    {
+      // generate the hashcode tied to this object for this type
+      newId = t.hashCode() + o.hashCode();
+      if (idSet.contains(newId))
+      {
+        Console.debug("Using an existing id for Type " + t.name()
+                + " and object " + o.toString() + ": '" + newId + "'");
+      }
+      else
+      {
+        idSet.add(newId);
+      }
+    }
+    count++;
+    return newId;
+  }
+
+  public static void NOTremoveId(IdType t, Object o)
+  {
+    if (o == null)
+    {
+      return;
+    }
+    Set<Long> idSet = typeMap.get(t);
+    long id = t.hashCode() + o.hashCode();
+    idSet.remove(id);
+  }
+
+  public static void NOTremoveId(IdType t, long id)
+  {
+    Set<Long> idSet = typeMap.get(t);
+    idSet.remove(id);
+  }
+
+}
diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 0ebd3c3..d4e34e7 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -20,16 +20,14 @@
  */
 package jalview.ws;
 
-import java.util.Locale;
-
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
-import java.util.StringTokenizer;
 import java.util.Vector;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -49,6 +47,8 @@ import jalview.gui.FeatureSettings;
 import jalview.gui.IProgressIndicator;
 import jalview.gui.OOMWarning;
 import jalview.util.DBRefUtils;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.MessageManager;
 import jalview.ws.seqfetcher.DbSourceProxy;
 import uk.ac.ebi.picr.model.UPEntry;
@@ -286,12 +286,12 @@ public class DBRefFetcher implements Runnable
       throw new Error(MessageManager
               .getString("error.implementation_error_must_init_dbsources"));
     }
-    long startTime = System.currentTimeMillis();
+    long progressId = IdUtils.newId(IdType.PROGRESS);
     if (progressWindow != null)
     {
       progressWindow.setProgressBar(
               MessageManager.getString("status.fetching_db_refs"),
-              startTime);
+              progressId);
     }
     try
     {
@@ -302,7 +302,8 @@ public class DBRefFetcher implements Runnable
       }
     } catch (Exception e)
     {
-      jalview.bin.Console.errPrintln("Couldn't locate PICR service instance.\n");
+      jalview.bin.Console
+              .errPrintln("Couldn't locate PICR service instance.\n");
       e.printStackTrace();
     }
 
@@ -316,7 +317,8 @@ public class DBRefFetcher implements Runnable
     while (sdataset.size() > 0 && db < dbSources.length)
     {
       int maxqlen = 1; // default number of queries made at one time
-      jalview.bin.Console.outPrintln("Verifying against " + dbSources[db].getDbName());
+      jalview.bin.Console
+              .outPrintln("Verifying against " + dbSources[db].getDbName());
 
       // iterate through db for each remaining un-verified sequence
       SequenceI[] currSeqs = new SequenceI[sdataset.size()];
@@ -482,7 +484,7 @@ public class DBRefFetcher implements Runnable
     {
       progressWindow.setProgressBar(
               MessageManager.getString("label.dbref_search_completed"),
-              startTime);
+              progressId);
     }
 
     for (FetchFinishedListenerI listener : listeners)
@@ -678,8 +680,8 @@ public class DBRefFetcher implements Runnable
           }
         }
 
-        jalview.bin.Console.outPrintln("Adding dbrefs to " + sequence.getName()
-                + " from " + dbSource + " sequence : "
+        jalview.bin.Console.outPrintln("Adding dbrefs to "
+                + sequence.getName() + " from " + dbSource + " sequence : "
                 + retrievedSeq.getName());
         sequence.transferAnnotation(retrievedSeq, mp);
 
diff --git a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
index 3b56a70..d1a226e 100644
--- a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
+++ b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
@@ -20,6 +20,18 @@
  */
 package jalview.ws.jws2;
 
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import compbio.data.sequence.FastaSequence;
+import compbio.metadata.Argument;
+import compbio.metadata.ChunkHolder;
+import compbio.metadata.JobStatus;
+import compbio.metadata.JobSubmissionException;
+import compbio.metadata.Option;
+import compbio.metadata.ResultNotAvailableException;
 import jalview.analysis.AlignSeq;
 import jalview.analysis.SeqsetUtils;
 import jalview.api.AlignViewportI;
@@ -33,25 +45,14 @@ import jalview.gui.AlignFrame;
 import jalview.gui.IProgressIndicator;
 import jalview.gui.IProgressIndicatorHandler;
 import jalview.schemes.ResidueProperties;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.workers.AlignCalcWorker;
 import jalview.ws.jws2.dm.AAConSettings;
 import jalview.ws.jws2.dm.JabaWsParamSet;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import compbio.data.sequence.FastaSequence;
-import compbio.metadata.Argument;
-import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.Option;
-import compbio.metadata.ResultNotAvailableException;
-
 public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
 {
 
@@ -219,7 +220,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
       if (guiProgress != null)
       {
         guiProgress.setProgressBar("JABA " + getServiceActionText(),
-                progressId = System.currentTimeMillis());
+                progressId = IdUtils.newId(IdType.PROGRESS));
       }
       rslt = submitToService(seqs);
       if (guiProgress != null)
@@ -259,11 +260,13 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
           {
             if (cancelJob(rslt))
             {
-              jalview.bin.Console.errPrintln("Cancelled AACon job: " + rslt);
+              jalview.bin.Console
+                      .errPrintln("Cancelled AACon job: " + rslt);
             }
             else
             {
-              jalview.bin.Console.errPrintln("FAILED TO CANCEL AACon job: " + rslt);
+              jalview.bin.Console
+                      .errPrintln("FAILED TO CANCEL AACon job: " + rslt);
             }
 
           } catch (Exception x)
@@ -445,7 +448,8 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
       }
       else
       {
-        jalview.bin.Console.errPrintln("Job " + id + " couldn't be cancelled.");
+        jalview.bin.Console
+                .errPrintln("Job " + id + " couldn't be cancelled.");
       }
     } catch (Exception q)
     {
diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 611aa79..f6e3104 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -20,6 +20,19 @@
  */
 package jalview.ws.jws2;
 
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+
+import compbio.data.msa.MsaWS;
+import compbio.metadata.Argument;
+import compbio.metadata.ChunkHolder;
+import compbio.metadata.JobStatus;
+import compbio.metadata.Preset;
 import jalview.analysis.AlignSeq;
 import jalview.bin.Console;
 import jalview.datamodel.Alignment;
@@ -33,6 +46,8 @@ import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.SplitFrame;
 import jalview.gui.WebserviceInfo;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.MessageManager;
 import jalview.ws.AWsJob;
 import jalview.ws.JobStateSummary;
@@ -40,20 +55,6 @@ import jalview.ws.WSClientI;
 import jalview.ws.jws2.dm.JabaWsParamSet;
 import jalview.ws.params.WsParamSetI;
 
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Vector;
-
-import javax.swing.JInternalFrame;
-
-import compbio.data.msa.MsaWS;
-import compbio.metadata.Argument;
-import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
-import compbio.metadata.Preset;
-
 class MsaWSThread extends AWS2Thread implements WSClientI
 {
   boolean submitGaps = false; // pass sequences including gaps to alignment
@@ -783,7 +784,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
   @Override
   public void parseResult()
   {
-    long progbar = System.currentTimeMillis();
+    long progbar = IdUtils.newId(IdType.PROGRESS);
     wsInfo.setProgressBar(
             MessageManager.getString("status.collecting_job_results"),
             progbar);
-- 
1.7.10.2