From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Thu, 26 Oct 2017 13:53:04 +0000 (+0100)
Subject: named most Jalview threads
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=422fd57f6ed8ff7a6744aee2497e90f80f46686f;p=jalview.git

named most Jalview threads
---

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 8ce597d..1855c3d 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -235,7 +235,7 @@ public class OverviewPanel extends Panel implements Runnable,
 
       updateRunning = true;
     }
-    Thread thread = new Thread(this);
+    Thread thread = new Thread(this, "OverviewUpdateThread");
     thread.start();
     repaint();
     updateRunning = false;
diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index fc1d359..ea6eda6 100644
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -117,7 +117,7 @@ public class PCAPanel extends EmbmenuFrame
             MessageManager.getString("label.principal_component_analysis"),
             475, 400);
 
-    Thread worker = new Thread(this);
+    Thread worker = new Thread(this, "PCACalcThread");
     worker.start();
   }
 
@@ -220,7 +220,7 @@ public class PCAPanel extends EmbmenuFrame
         ScoreModelI scoreModel = ScoreModels.getInstance()
                 .getDefaultModel(false);
         pcaModel.setScoreModel(scoreModel);
-        new Thread(this).start();
+        new Thread(this, "PCARecalcThread").start();
       }
     }
     else if (evt.getSource() == protSetting)
@@ -231,7 +231,7 @@ public class PCAPanel extends EmbmenuFrame
         ScoreModelI scoreModel = ScoreModels.getInstance()
                 .getDefaultModel(true);
         pcaModel.setScoreModel(scoreModel);
-        new Thread(this).start();
+        new Thread(this, "PCARecalcThread").start();
       }
     }
   }
diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index bd36b0d..c7d8157 100644
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -89,7 +89,7 @@ public class RedundancyPanel extends SliderPanel
 
     frame.addWindowListener(this);
 
-    Thread worker = new Thread(this);
+    Thread worker = new Thread(this, "RedundancyCalcThread");
     worker.start();
   }
 
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 9ec0033..245a63c 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,9 +20,6 @@
  */
 package jalview.bin;
 
-import groovy.lang.Binding;
-import groovy.util.GroovyScriptEngine;
-
 import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -66,6 +63,9 @@ import java.util.Vector;
 
 import javax.swing.UIManager;
 
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
 /**
  * Main class for Jalview Application <br>
  * <br>
@@ -155,7 +155,7 @@ public class Jalview
             running--;
           }
         }
-      }).start();
+      }, "FeatureFetcherThread").start();
     }
 
     public synchronized boolean allFinished()
@@ -970,7 +970,7 @@ public class Jalview
     }
     try
     {
-      Map<String, Object> vbinding = new HashMap<String, Object>();
+      Map<String, Object> vbinding = new HashMap<>();
       vbinding.put("Jalview", this);
       if (af != null)
       {
@@ -1036,7 +1036,7 @@ public class Jalview
                         + nickname + "|" + url);
         if (source == null)
         {
-          source = new Vector<String>();
+          source = new Vector<>();
         }
         source.addElement(nickname);
       }
@@ -1054,7 +1054,7 @@ public class Jalview
       System.out.println("adding source '" + data + "'");
       if (source == null)
       {
-        source = new Vector<String>();
+        source = new Vector<>();
       }
       source.addElement(data);
     }
diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 00446f2..82cba86 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -76,9 +76,9 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   private static final String ALPHACARBON = "CA";
 
-  private List<String> chainNames = new ArrayList<String>();
+  private List<String> chainNames = new ArrayList<>();
 
-  private Hashtable<String, String> chainFile = new Hashtable<String, String>();
+  private Hashtable<String, String> chainFile = new Hashtable<>();
 
   /*
    * Object through which we talk to Chimera
@@ -106,7 +106,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   /*
    * Map of ChimeraModel objects keyed by PDB full local file name
    */
-  private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>();
+  private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<>();
 
   String lastHighlightCommand;
 
@@ -133,7 +133,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     String file = pe.getFile();
     try
     {
-      List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>();
+      List<ChimeraModel> modelsToMap = new ArrayList<>();
       List<ChimeraModel> oldList = viewer.getModelList();
       boolean alreadyOpen = false;
 
@@ -226,7 +226,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           // exit thread if Chimera Viewer is closed in Jalview
         }
       }
-    });
+    }, "ChimeraMonitorThread");
     chimeraMonitor.start();
   }
 
@@ -857,7 +857,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   protected List<AtomSpec> convertStructureResiduesToAlignment(
           List<String> structureSelection)
   {
-    List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
+    List<AtomSpec> atomSpecs = new ArrayList<>();
     for (String atomSpec : structureSelection)
     {
       try
diff --git a/src/jalview/fts/core/GFTSPanel.java b/src/jalview/fts/core/GFTSPanel.java
index c0d005f..e0bf9b2 100644
--- a/src/jalview/fts/core/GFTSPanel.java
+++ b/src/jalview/fts/core/GFTSPanel.java
@@ -90,7 +90,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
 
   protected IProgressIndicator progressIndicator;
 
-  protected JComboBox<FTSDataColumnI> cmb_searchTarget = new JComboBox<FTSDataColumnI>();
+  protected JComboBox<FTSDataColumnI> cmb_searchTarget = new JComboBox<>();
 
   protected JButton btn_ok = new JButton();
 
@@ -147,7 +147,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
 
   protected int pageLimit;
 
-  protected HashSet<String> paginatorCart = new HashSet<String>();
+  protected HashSet<String> paginatorCart = new HashSet<>();
 
   private static final int MIN_WIDTH = 670;
 
@@ -267,7 +267,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
   private void jbInit() throws Exception
   {
 
-    txt_search = new JvCacheableInputBox<String>(getCacheKey());
+    txt_search = new JvCacheableInputBox<>(getCacheKey());
     populateCmbSearchTargetOptions();
     Integer width = getTempUserPrefs().get("FTSPanel.width") == null ? 800
             : getTempUserPrefs().get("FTSPanel.width");
@@ -797,7 +797,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
    */
   public void populateCmbSearchTargetOptions()
   {
-    List<FTSDataColumnI> searchableTargets = new ArrayList<FTSDataColumnI>();
+    List<FTSDataColumnI> searchableTargets = new ArrayList<>();
     try
     {
       Collection<FTSDataColumnI> foundFTSTargets = getFTSRestClient()
@@ -826,7 +826,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
   public void transferToSequenceFetcher(String ids)
   {
     seqFetcher.getTextArea().setText(ids);
-    Thread worker = new Thread(seqFetcher);
+    Thread worker = new Thread(seqFetcher, "GFTSSeqFetcherThread");
     worker.start();
   }
 
diff --git a/src/jalview/fts/service/pdb/PDBFTSPanel.java b/src/jalview/fts/service/pdb/PDBFTSPanel.java
index 19f7db4..753cc2e 100644
--- a/src/jalview/fts/service/pdb/PDBFTSPanel.java
+++ b/src/jalview/fts/service/pdb/PDBFTSPanel.java
@@ -39,7 +39,7 @@ public class PDBFTSPanel extends GFTSPanel
   private static String defaultFTSFrameTitle = MessageManager
           .getString("label.pdb_sequence_fetcher");
 
-  private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
+  private static Map<String, Integer> tempUserPrefs = new HashMap<>();
 
   private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS";
 
@@ -188,7 +188,7 @@ public class PDBFTSPanel extends GFTSPanel
     // mainFrame.dispose();
     disableActionButtons();
     StringBuilder selectedIds = new StringBuilder();
-    HashSet<String> selectedIdsSet = new HashSet<String>();
+    HashSet<String> selectedIdsSet = new HashSet<>();
     int primaryKeyColIndex = 0;
     try
     {
@@ -220,7 +220,7 @@ public class PDBFTSPanel extends GFTSPanel
     String ids = selectedIds.toString();
     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
     seqFetcher.getTextArea().setText(ids);
-    Thread worker = new Thread(seqFetcher);
+    Thread worker = new Thread(seqFetcher, "PDBFTSSeqFetcherThread");
     worker.start();
     delayAndEnableActionButtons();
   }
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2ac6b19..fe0d220 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4154,7 +4154,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
         buildingMenu = false;
       }
-    }).start();
+    }, "BuildWebServiceThread").start();
 
   }
 
@@ -4262,7 +4262,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
           final String source)
   {
-    new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+    new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this),
+            "CrossReferencesThread")
             .start();
   }
 
@@ -4541,7 +4542,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             ex.printStackTrace();
           }
         }
-      }).start();
+      }, "DropFileThread").start();
     }
   }
 
@@ -4912,7 +4913,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             });
             dbRefFetcher.fetchDBRefs(false);
           }
-        }).start();
+        }, "BuildFetchDBMenuThread").start();
 
       }
 
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index fef7451..d5eb2ae 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -218,7 +218,7 @@ public class AppJmol extends StructureViewerBase
     setSize(400, 400); // probably should be a configurable/dynamic default here
     initMenus();
     addingStructures = false;
-    worker = new Thread(this);
+    worker = new Thread(this, "OpenJmolThread");
     worker.start();
 
     this.addInternalFrameListener(new InternalFrameAdapter()
diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 89de2e8..48565eb 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -272,7 +272,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     initMenus();
 
     addingStructures = false;
-    worker = new Thread(this);
+    worker = new Thread(this, "OpenChimeraThread");
     worker.start();
 
     this.addInternalFrameListener(new InternalFrameAdapter()
diff --git a/src/jalview/gui/Console.java b/src/jalview/gui/Console.java
index 4c019a6..5fee61f 100644
--- a/src/jalview/gui/Console.java
+++ b/src/jalview/gui/Console.java
@@ -138,15 +138,15 @@ public class Console extends WindowAdapter
 
     // Starting two seperate threads to read from the PipedInputStreams
     //
-    reader = new Thread(this);
+    reader = new Thread(this, "ConsoleReader1Thread");
     reader.setDaemon(true);
     reader.start();
     //
-    reader2 = new Thread(this);
+    reader2 = new Thread(this, "ConsoleReader2Thread");
     reader2.setDaemon(true);
     reader2.start();
     // and a thread to append text to the textarea
-    textAppender = new Thread(this);
+    textAppender = new Thread(this, "ConsoleTextAppendThread");
     textAppender.setDaemon(true);
     textAppender.start();
   }
@@ -255,7 +255,7 @@ public class Console extends WindowAdapter
     // We do it with a seperate Thread becasue we don't wan't to break a Thread
     // used by the Console.
     System.out.println("\nLets throw an error on this console");
-    errorThrower = new Thread(this);
+    errorThrower = new Thread(this, "ConsoleErrorLogThread");
     errorThrower.setDaemon(true);
     errorThrower.start();
   }
diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index 8570ac3..a1b67e7 100644
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -38,7 +38,6 @@ import java.util.Vector;
 
 import javax.swing.JCheckBox;
 import javax.swing.JLabel;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JTextField;
 import javax.swing.ListSelectionModel;
@@ -125,7 +124,7 @@ public class DasSourceBrowser extends GDasSourceBrowser
   {
     if (sourceRegistry == null)
     {
-      Thread worker = new Thread(this);
+      Thread worker = new Thread(this, "PaintDasThread");
       worker.start();
     }
   }
@@ -352,7 +351,7 @@ public class DasSourceBrowser extends GDasSourceBrowser
       }
     }
 
-    Vector<jalviewSourceI> selected = new Vector<jalviewSourceI>();
+    Vector<jalviewSourceI> selected = new Vector<>();
     for (String source : selectedSources)
     {
       jalviewSourceI srce = sourceRegistry.getSource(source);
@@ -369,16 +368,16 @@ public class DasSourceBrowser extends GDasSourceBrowser
   {
     saveProperties(jalview.bin.Cache.applicationProperties);
 
-    Thread worker = new Thread(this);
+    Thread worker = new Thread(this, "RepaintDasThread");
     worker.start();
   }
 
   private void setCapabilities(DasSourceRegistryI sourceRegistry2)
   {
-    Vector<String> authority = new Vector<String>();
-    Vector<String> type = new Vector<String>();
-    Vector<String> label = new Vector<String>();
-    Vector<String> taxIds = new Vector<String>();
+    Vector<String> authority = new Vector<>();
+    Vector<String> type = new Vector<>();
+    Vector<String> label = new Vector<>();
+    Vector<String> taxIds = new Vector<>();
     authority.add("Any");
     type.add("Any");
     label.add("Any");
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 2d1ba12..f90752b 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -456,7 +456,7 @@ public class Desktop extends jalview.jbgui.GDesktop
                 fileFormat);
         Cache.log.debug("Filechooser init thread finished.");
       }
-    }).start();
+    }, "InitFileChooserThread").start();
     // Add the service change listener
     changeSupport.addJalviewPropertyChangeListener("services",
             new PropertyChangeListener()
@@ -575,7 +575,7 @@ public class Desktop extends jalview.jbgui.GDesktop
             Desktop.instance.setProgressBar(null, now);
             jvnews.showNews();
           }
-        }).start();
+        }, "ShowNewsWindowThread").start();
       }
     }
   }
@@ -1271,7 +1271,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       {
         new SplashScreen(true);
       }
-    }).start();
+    }, "ShowAboutMenuThread").start();
   }
 
   public StringBuffer getAboutMessage(boolean shortv)
@@ -1613,7 +1613,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           }
           setProgressBar(null, choice.hashCode());
         }
-      }).start();
+      }, "SaveJalviewProjectThread").start();
     }
   }
 
@@ -1681,7 +1681,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           }
           setProgressBar(null, choice.hashCode());
         }
-      }).start();
+      }, "LoadJalviewProjectThread").start();
     }
   }
 
@@ -2191,7 +2191,7 @@ public class Desktop extends jalview.jbgui.GDesktop
                     dsktp.v_client.initial_update();
                   }
 
-                });
+                }, "VamsasSessionThread");
                 rthr.start();
               }
             };
@@ -2311,7 +2311,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
     // javax.swing.SwingUtilities.invokeLater(jvq);
-    new Thread(jvq).start();
+    new Thread(jvq, "CheckQuestionnaireThread").start();
   }
 
   public void checkURLLinks()
@@ -2424,7 +2424,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       this.showMemoryUsage = showMemory;
       if (showMemory)
       {
-        Thread worker = new Thread(this);
+        Thread worker = new Thread(this, "ShowMemoryUsageThread");
         worker.start();
       }
       repaint();
@@ -2849,7 +2849,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       }
       // JAL-940 - disabled JWS1 service configuration - always start discoverer
       // until we phase out completely
-      (t0 = new Thread(discoverer)).start();
+      (t0 = new Thread(discoverer, "DiscovererThread")).start();
     }
 
     if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
@@ -3005,7 +3005,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           progress.setProgressBar(null, this.hashCode());
         }
       }
-    }).start();
+    }, "OpenURLThread").start();
   }
 
   public static WsParamSetManager wsparamManager = null;
diff --git a/src/jalview/gui/JalviewDialog.java b/src/jalview/gui/JalviewDialog.java
index 05f5ffc..a6f2d2a 100644
--- a/src/jalview/gui/JalviewDialog.java
+++ b/src/jalview/gui/JalviewDialog.java
@@ -66,7 +66,7 @@ public abstract class JalviewDialog extends JPanel
           frame.setVisible(true);
         }
 
-      }).start();
+      }, "UnblockedDialogThread").start();
     }
     else
     {
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 9ddb751..a39944d 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -304,7 +304,7 @@ public class OverviewPanel extends JPanel
       return;
     }
 
-    Thread thread = new Thread(this);
+    Thread thread = new Thread(this, "UpdateOverviewThread");
     thread.start();
     repaint();
 
diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 31c20ed..aa07b7c 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -352,7 +352,7 @@ public abstract class StructureViewerBase extends GStructureViewer
             // and call ourselves again.
             addStructure(pdbentry, seqs, chains, align, alignFrame);
           }
-        }).start();
+        }, "Adding3DStructureQueueThread").start();
         return;
       }
     }
@@ -363,7 +363,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     addingStructures = true;
     _started = false;
     alignAddedStructures = align;
-    worker = new Thread(this);
+    worker = new Thread(this, "Adding3DStructureThread");
     worker.start();
     return;
   }
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 7dc1a99..6780921 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -542,7 +542,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    */
   void startPrinting()
   {
-    Thread thread = new Thread(this);
+    Thread thread = new Thread(this, "PrintTreeCanvasThread");
     thread.start();
   }
 
@@ -981,7 +981,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
       Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
 
-      Vector<SequenceI> sequences = new Vector<SequenceI>();
+      Vector<SequenceI> sequences = new Vector<>();
 
       for (int j = 0; j < l.size(); j++)
       {
diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index d2086e0..f855474 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -326,7 +326,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
         Cache.log.info("Jalview finished updating to the Vamsas Session.");
       }
 
-    });
+    }, "UpdateVamsasThread");
     udthread.start();
   }
 
diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java
index 2fc08e1..be812b5 100644
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.java
@@ -39,7 +39,6 @@ import java.util.Vector;
 import javax.swing.JComponent;
 import javax.swing.JEditorPane;
 import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.JTabbedPane;
@@ -345,12 +344,13 @@ public class WebserviceInfo extends GWebserviceInfo
     AnimatedPanel ap = new AnimatedPanel();
     titlePanel.add(ap, BorderLayout.CENTER);
 
-    Thread thread = new Thread(ap);
+    Thread thread = new Thread(ap, "AnimatedPanelThread");
     thread.start();
     final WebserviceInfo thisinfo = this;
     frame.addInternalFrameListener(
             new javax.swing.event.InternalFrameAdapter()
             {
+              @Override
               public void internalFrameClosed(
                       javax.swing.event.InternalFrameEvent evt)
               {
@@ -676,6 +676,7 @@ public class WebserviceInfo extends GWebserviceInfo
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void cancel_actionPerformed(ActionEvent e)
   {
     if (!serviceIsCancellable)
@@ -707,6 +708,7 @@ public class WebserviceInfo extends GWebserviceInfo
   {
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
@@ -756,6 +758,7 @@ public class WebserviceInfo extends GWebserviceInfo
 
     BufferedImage offscreen;
 
+    @Override
     public void run()
     {
       startTime = System.currentTimeMillis();
@@ -865,6 +868,7 @@ public class WebserviceInfo extends GWebserviceInfo
       }
     }
 
+    @Override
     public void paintComponent(Graphics g1)
     {
       drawPanel();
@@ -880,6 +884,7 @@ public class WebserviceInfo extends GWebserviceInfo
     renderAsHtml = b;
   }
 
+  @Override
   public void hyperlinkUpdate(HyperlinkEvent e)
   {
     Desktop.hyperlinkUpdate(e);
diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java
index 850ef21..dc3cadd 100644
--- a/src/jalview/gui/WsPreferences.java
+++ b/src/jalview/gui/WsPreferences.java
@@ -37,7 +37,6 @@ import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JLabel;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JTable;
 import javax.swing.JTextField;
@@ -68,12 +67,12 @@ public class WsPreferences extends GWsPreferences
     wsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls();
     if (!wsUrls.isEmpty())
     {
-      oldUrls = new Vector<String>(wsUrls);
+      oldUrls = new Vector<>(wsUrls);
     }
     else
     {
       oldUrls = null;
-      wsUrls = new Vector<String>();
+      wsUrls = new Vector<>();
     }
     wsList.setDefaultRenderer(Integer.class, new JabaWSStatusRenderer());
     wsList.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
@@ -81,12 +80,12 @@ public class WsPreferences extends GWsPreferences
     rsbsUrls = jalview.ws.rest.RestClient.getRsbsDescriptions();
     if (rsbsUrls != null)
     {
-      oldRsbsUrls = new Vector<String>(rsbsUrls);
+      oldRsbsUrls = new Vector<>(rsbsUrls);
     }
     else
     {
       oldRsbsUrls = null;
-      rsbsUrls = new Vector<String>();
+      rsbsUrls = new Vector<>();
     }
     updateRsbsList();
     enableEnfinServices.setSelected(
@@ -568,7 +567,7 @@ public class WsPreferences extends GWsPreferences
         updateWsMenuConfig(false);
         refreshWsMenu(true);
       }
-    }).start();
+    }, "RefreshWebServicesThread").start();
 
   }
 
@@ -604,7 +603,7 @@ public class WsPreferences extends GWsPreferences
           progressBar.setVisible(false);
           validate();
         }
-      }).start();
+      }, "RefreshWebServicesMenuProgressBarThread").start();
 
     }
     else
@@ -627,7 +626,7 @@ public class WsPreferences extends GWsPreferences
           Desktop.instance.setProgressBar(null, ct);
         }
 
-      }).start();
+      }, "RefreshWebServicesMenuThread").start();
     }
   }
 
@@ -676,7 +675,7 @@ public class WsPreferences extends GWsPreferences
         updateWsMenuConfig(false);
         refreshWsMenu(showProgressInDialog);
       }
-    }).start();
+    }, "UpdateAndRefreshWebServicesMenuThread").start();
 
   }
 }
diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 52ce845..045fc7e 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -84,7 +84,7 @@ public class BioJsHTMLOutput extends HTMLOutput
       e.printStackTrace();
       return;
     }
-    new Thread(this).start();
+    new Thread(this, "ExportBioJsHTMLThread").start();
 
   }
 
@@ -94,7 +94,7 @@ public class BioJsHTMLOutput extends HTMLOutput
     File directory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
     Objects.requireNonNull(dirName, "dirName MUST not be null!");
     Objects.requireNonNull(directory, "directory MUST not be null!");
-    TreeMap<String, File> versionFileMap = new TreeMap<String, File>();
+    TreeMap<String, File> versionFileMap = new TreeMap<>();
 
     for (File file : directory.listFiles())
     {
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 26641b1..50bcbe1 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -104,7 +104,7 @@ public class FileLoader implements Runnable
     this.protocol = protocol;
     this.format = format;
 
-    final Thread loader = new Thread(this);
+    final Thread loader = new Thread(this, "LoadFileThread");
 
     SwingUtilities.invokeLater(new Runnable()
     {
@@ -183,7 +183,7 @@ public class FileLoader implements Runnable
    */
   protected AlignFrame _LoadFileWaitTillLoaded()
   {
-    Thread loader = new Thread(this);
+    Thread loader = new Thread(this, "LoadFileWithWaitingThread");
     loader.start();
 
     while (loader.isAlive())
diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index 948578a..87be23e 100644
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -67,7 +67,7 @@ public class HtmlSvgOutput extends HTMLOutput
       e.printStackTrace();
       return;
     }
-    new Thread(this).start();
+    new Thread(this, "ExportSvgHTMLThread").start();
   }
 
   public int printUnwrapped(int pwidth, int pheight, int pi,
diff --git a/src/jalview/javascript/JSFunctionExec.java b/src/jalview/javascript/JSFunctionExec.java
index 083cd26..c516a9f 100644
--- a/src/jalview/javascript/JSFunctionExec.java
+++ b/src/jalview/javascript/JSFunctionExec.java
@@ -261,7 +261,8 @@ public class JSFunctionExec implements Runnable
     {
       if (executor == null)
       {
-        executor = new Thread(new JSFunctionExec(jvlite));
+        executor = new Thread(new JSFunctionExec(jvlite),
+                "JavaScriptThread");
         executor.start();
       }
       synchronized (jsExecQueue)
diff --git a/src/jalview/util/AWTConsole.java b/src/jalview/util/AWTConsole.java
index 6698414..be03591 100644
--- a/src/jalview/util/AWTConsole.java
+++ b/src/jalview/util/AWTConsole.java
@@ -72,10 +72,10 @@ public class AWTConsole extends WindowAdapter
     // create all components and add them
     frame = new Frame("Java Console");
     Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
-    Dimension frameSize = new Dimension((int) (screenSize.width / 2),
-            (int) (screenSize.height / 2));
-    int x = (int) (frameSize.width / 2);
-    int y = (int) (frameSize.height / 2);
+    Dimension frameSize = new Dimension(screenSize.width / 2,
+            screenSize.height / 2);
+    int x = frameSize.width / 2;
+    int y = frameSize.height / 2;
     frame.setBounds(x, y, frameSize.width, frameSize.height);
 
     textArea = new TextArea();
@@ -125,11 +125,11 @@ public class AWTConsole extends WindowAdapter
 
     // Starting two seperate threads to read from the PipedInputStreams
     //
-    reader = new Thread(this);
+    reader = new Thread(this, "AWTConsoleReader1Thread");
     reader.setDaemon(true);
     reader.start();
     //
-    reader2 = new Thread(this);
+    reader2 = new Thread(this, "AWTConsoleReader2Thread");
     reader2.setDaemon(true);
     reader2.start();
 
@@ -142,17 +142,20 @@ public class AWTConsole extends WindowAdapter
             .getLocalGraphicsEnvironment();
     String[] fontNames = ge.getAvailableFontFamilyNames();
     for (int n = 0; n < fontNames.length; n++)
+    {
       System.out.println(fontNames[n]);
+    }
     // Testing part: simple an error thrown anywhere in this JVM will be printed
     // on the Console
     // We do it with a seperate Thread becasue we don't wan't to break a Thread
     // used by the Console.
     System.out.println("\nLets throw an error on this console");
-    errorThrower = new Thread(this);
+    errorThrower = new Thread(this, "AWTConsoleErrorLogThread");
     errorThrower.setDaemon(true);
     errorThrower.start();
   }
 
+  @Override
   public synchronized void windowClosed(WindowEvent evt)
   {
     quit = true;
@@ -174,17 +177,20 @@ public class AWTConsole extends WindowAdapter
     System.exit(0);
   }
 
+  @Override
   public synchronized void windowClosing(WindowEvent evt)
   {
     frame.setVisible(false); // default behaviour of JFrame
     frame.dispose();
   }
 
+  @Override
   public synchronized void actionPerformed(ActionEvent evt)
   {
     textArea.setText("");
   }
 
+  @Override
   public synchronized void run()
   {
     try
@@ -203,7 +209,9 @@ public class AWTConsole extends WindowAdapter
           textArea.append(input);
         }
         if (quit)
+        {
           return;
+        }
       }
 
       while (Thread.currentThread() == reader2)
@@ -220,7 +228,9 @@ public class AWTConsole extends WindowAdapter
           textArea.append(input);
         }
         if (quit)
+        {
           return;
+        }
       }
     } catch (Exception e)
     {
@@ -251,7 +261,9 @@ public class AWTConsole extends WindowAdapter
     {
       int available = in.available();
       if (available == 0)
+      {
         break;
+      }
       byte b[] = new byte[available];
       in.read(b);
       input = input + new String(b, 0, b.length);
diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index fb8864d..2b7c6df 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -117,7 +117,7 @@ public class DBRefFetcher implements Runnable
           DbSourceProxy[] sources, FeatureSettings featureSettings,
           boolean isNucleotide)
   {
-    listeners = new ArrayList<FetchFinishedListenerI>();
+    listeners = new ArrayList<>();
     this.progressWindow = progressIndicatorFrame;
     alseqs = new SequenceI[seqs.length];
     SequenceI[] ds = new SequenceI[seqs.length];
@@ -163,7 +163,7 @@ public class DBRefFetcher implements Runnable
   {
     // af.featureSettings_actionPerformed(null);
     String[] defdb = null;
-    List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
+    List<DbSourceProxy> selsources = new ArrayList<>();
     Vector<jalviewSourceI> dasselsrc = (featureSettings != null)
             ? featureSettings.getSelectedSources()
             : new DasSourceBrowser().getSelectedSources();
@@ -189,7 +189,7 @@ public class DBRefFetcher implements Runnable
     {
       defdb = DBRefSource.PROTEINDBS;
     }
-    List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
+    List<DbSourceProxy> srces = new ArrayList<>();
     for (String ddb : defdb)
     {
       List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
@@ -267,7 +267,7 @@ public class DBRefFetcher implements Runnable
     // TODO can we not simply write
     // if (waitTillFinished) { run(); } else { new Thread(this).start(); }
 
-    Thread thread = new Thread(this);
+    Thread thread = new Thread(this, "FetchDBRefThread");
     thread.start();
     running = true;
 
@@ -309,14 +309,14 @@ public class DBRefFetcher implements Runnable
       }
       else if (seqs == null)
       {
-        seqs = new Vector<SequenceI>();
+        seqs = new Vector<>();
         seqs.addElement(seq);
       }
 
     }
     else
     {
-      seqs = new Vector<SequenceI>();
+      seqs = new Vector<>();
       seqs.addElement(seq);
     }
 
@@ -355,9 +355,9 @@ public class DBRefFetcher implements Runnable
       e.printStackTrace();
     }
 
-    Vector<SequenceI> sdataset = new Vector<SequenceI>(
+    Vector<SequenceI> sdataset = new Vector<>(
             Arrays.asList(dataset));
-    List<String> warningMessages = new ArrayList<String>();
+    List<String> warningMessages = new ArrayList<>();
 
     int db = 0;
     while (sdataset.size() > 0 && db < dbSources.length)
@@ -369,8 +369,8 @@ public class DBRefFetcher implements Runnable
       SequenceI[] currSeqs = new SequenceI[sdataset.size()];
       sdataset.copyInto(currSeqs);// seqs that are to be validated against
       // dbSources[db]
-      Vector<String> queries = new Vector<String>(); // generated queries curSeq
-      seqRefs = new Hashtable<String, Vector<SequenceI>>();
+      Vector<String> queries = new Vector<>(); // generated queries curSeq
+      seqRefs = new Hashtable<>();
 
       int seqIndex = 0;
 
@@ -572,7 +572,7 @@ public class DBRefFetcher implements Runnable
     {
       // Work out which sequences this sequence matches,
       // taking into account all accessionIds and names in the file
-      Vector<SequenceI> sequenceMatches = new Vector<SequenceI>();
+      Vector<SequenceI> sequenceMatches = new Vector<>();
       // look for corresponding accession ids
       DBRefEntry[] entryRefs = DBRefUtils
               .selectRefs(retrievedSeq.getDBRefs(), new String[]
@@ -824,7 +824,7 @@ public class DBRefFetcher implements Runnable
    */
   private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
   {
-    Vector<SequenceI> nseq = new Vector<SequenceI>();
+    Vector<SequenceI> nseq = new Vector<>();
     for (int i = 0; sequencesArray != null
             && i < sequencesArray.length; i++)
     {
diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index c661e2c..06d176e 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -212,7 +212,8 @@ public class DasSequenceFeatureFetcher
 
       if (reply == JvOptionPane.YES_OPTION)
       {
-        Thread thread = new Thread(new FetchDBRefs());
+        Thread thread = new Thread(new FetchDBRefs(),
+                "FetchDBReferenceManagerThread");
         thread.start();
       }
       else
@@ -230,7 +231,7 @@ public class DasSequenceFeatureFetcher
   private void _startFetching()
   {
     running = true;
-    new Thread(new FetchSeqFeatures()).start();
+    new Thread(new FetchSeqFeatures(), "FetchSeqFeaturesThread").start();
   }
 
   class FetchSeqFeatures implements Runnable
diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java
index ea883c8..51e7b1a 100644
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -379,7 +379,7 @@ public class Discoverer implements Runnable
   public void run()
   {
     final Discoverer discoverer = this;
-    Thread discoverThread = new Thread()
+    Thread discoverThread = new Thread() // no function?
     {
       @Override
       public void run()
diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 5319eab..fe303f8 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -178,7 +178,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     running = true;
 
     // first set up exclusion list if needed
-    final Set<String> ignoredServices = new HashSet<String>();
+    final Set<String> ignoredServices = new HashSet<>();
     for (String ignored : Cache
             .getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|"))
     {
@@ -217,9 +217,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     {
       validServiceUrls.removeAllElements();
     }
-    ArrayList<String> svctypes = new ArrayList<String>();
+    ArrayList<String> svctypes = new ArrayList<>();
 
-    List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
+    List<JabaWsServerQuery> qrys = new ArrayList<>();
     for (final String jwsserver : getServiceUrls())
     {
       JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver);
@@ -237,7 +237,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
       }
       qrys.add(squery);
-      new Thread(squery).start();
+      new Thread(squery, "JabaQueryThread").start();
     }
     boolean finished = true;
     do
@@ -285,7 +285,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
                   + svctypes.indexOf(svc.serviceType);
         }
         jalview.util.QuickSort.sort(spos, svcs);
-        services = new Vector<Jws2Instance>();
+        services = new Vector<>();
         for (Jws2Instance svc : svcs)
         {
           if (!ignoredServices.contains(svc.serviceType))
@@ -312,7 +312,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (services == null)
     {
-      services = new Vector<Jws2Instance>();
+      services = new Vector<>();
     }
     System.out.println(
             "Discovered service: " + jwsservers + " " + service.toString());
@@ -329,7 +329,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     service.hasParameters();
     if (validServiceUrls == null)
     {
-      validServiceUrls = new Vector<String>();
+      validServiceUrls = new Vector<>();
     }
     validServiceUrls.add(jwsservers);
   }
@@ -363,10 +363,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
      * for moment we keep them separate.
      */
     JMenu atpoint;
-    List<Jws2Instance> enumerableServices = new ArrayList<Jws2Instance>();
+    List<Jws2Instance> enumerableServices = new ArrayList<>();
     // jws2al.removeAll();
-    Map<String, Jws2Instance> preferredHosts = new HashMap<String, Jws2Instance>();
-    Map<String, List<Jws2Instance>> alternates = new HashMap<String, List<Jws2Instance>>();
+    Map<String, Jws2Instance> preferredHosts = new HashMap<>();
+    Map<String, List<Jws2Instance>> alternates = new HashMap<>();
     for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
     {
       if (!isRecalculable(service.action))
@@ -395,7 +395,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
         {
           if (ph == null)
           {
-            ph = new ArrayList<Jws2Instance>();
+            ph = new ArrayList<>();
           }
           ph.add(service);
           alternates.put(service.serviceType, ph);
@@ -458,7 +458,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
                   changeSupport.firePropertyChange("services",
                           new Vector<Jws2Instance>(), services);
                 };
-              }).start();
+              }, "LoadPreferredServiceThread").start();
 
             }
           });
@@ -483,17 +483,17 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
      */
     JMenu atpoint;
 
-    List<String> hostLabels = new ArrayList<String>();
-    Hashtable<String, String> lasthostFor = new Hashtable<String, String>();
-    Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<String, ArrayList<Jws2Instance>>();
-    ArrayList<String> hostlist = new ArrayList<String>();
+    List<String> hostLabels = new ArrayList<>();
+    Hashtable<String, String> lasthostFor = new Hashtable<>();
+    Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<>();
+    ArrayList<String> hostlist = new ArrayList<>();
     for (Jws2Instance service : enumerableServices)
     {
       ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
       if (hostservices == null)
       {
         hosts.put(service.getHost(),
-                hostservices = new ArrayList<Jws2Instance>());
+                hostservices = new ArrayList<>());
         hostlist.add(service.getHost());
       }
       hostservices.add(service);
@@ -581,7 +581,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (args.length > 0)
     {
-      testUrls = new ArrayList<String>();
+      testUrls = new ArrayList<>();
       for (String url : args)
       {
         testUrls.add(url);
@@ -685,7 +685,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       // return test urls, if there are any, instead of touching cache
       return testUrls;
     }
-    List<String> urls = new ArrayList<String>();
+    List<String> urls = new ArrayList<>();
 
     if (this.preferredUrl != null)
     {
@@ -734,7 +734,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   public Vector<Jws2Instance> getServices()
   {
     return (services == null) ? new Vector<Jws2Instance>()
-            : new Vector<Jws2Instance>(services);
+            : new Vector<>(services);
   }
 
   /**
@@ -839,7 +839,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (urlsWithoutServices == null)
     {
-      urlsWithoutServices = new Vector<String>();
+      urlsWithoutServices = new Vector<>();
     }
 
     if ((invalidServiceUrls == null
@@ -859,7 +859,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (invalidServiceUrls == null)
     {
-      invalidServiceUrls = new Vector<String>();
+      invalidServiceUrls = new Vector<>();
     }
     if (!invalidServiceUrls.contains(jwsservers))
     {
@@ -947,7 +947,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    */
   public Jws2Instance getPreferredServiceFor(String[] serviceURLs)
   {
-    HashSet<String> urls = new HashSet<String>();
+    HashSet<String> urls = new HashSet<>();
     urls.addAll(Arrays.asList(serviceURLs));
     Jws2Instance match = null;
     if (services != null)
@@ -974,7 +974,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     return match;
   }
 
-  Map<String, Map<String, String>> preferredServiceMap = new HashMap<String, Map<String, String>>();;
+  Map<String, Map<String, String>> preferredServiceMap = new HashMap<>();;
 
   /**
    * get current preferred service of the given type, or global default
@@ -1026,12 +1026,12 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
     if (preferredServiceMap == null)
     {
-      preferredServiceMap = new HashMap<String, Map<String, String>>();
+      preferredServiceMap = new HashMap<>();
     }
     Map<String, String> prefmap = preferredServiceMap.get(afid);
     if (prefmap == null)
     {
-      prefmap = new HashMap<String, String>();
+      prefmap = new HashMap<>();
       preferredServiceMap.put(afid, prefmap);
     }
     prefmap.put(serviceType, selectedServer.getHost());