From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 4 Mar 2022 17:19:40 +0000 (+0000)
Subject: Merge branch 'develop' into releases/Release_2_11_2_Branch
X-Git-Tag: Release_2_11_2_0~6
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=9d2d74b49cd06966eaad8796c87386be1e296057;hp=63bb374ef5af0747f944d6fce14d49514f880597

Merge branch 'develop' into releases/Release_2_11_2_Branch
---

diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html
index d091272..a33a076 100755
--- a/help/help/html/features/preferences.html
+++ b/help/help/html/features/preferences.html
@@ -236,6 +236,13 @@
     installed the chosen viewer in a non-standard location, you can specify it
     here, by entering the full path to its executable.<br/>For Chimera, locate the path to the chimera program, similarly for ChimeraX and Pymol. Rather than typing in the path, you can also <em>double-click this field</em> to open a file chooser dialog.</p>
   <p>
+    <em>Sequence &lt;-&gt; Structure Mapping Method</em> - This setting controls whether
+    Jalview attempts to retrieve mappings between Uniprot protein
+    sequences and 3D structures in the PDBe with SIFTS, or constructs a
+    mapping by conservative alignment between the sequences and chains
+    in the 3D structure data using the Needleman and Wunsch algorithm.
+    SIFTS is enabled by default. 
+  <p>
     <em>PDB Fields shown in Search and Structure Summaries</em> - ticks
     in this table indicate fields shown by default when browsing results
     of a free text search via the PDB sequence fetcher, or 3D structures
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 8177708..d5e5dec 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -139,7 +139,13 @@ li:before {
             than anonymous 'Java' icons
           </li>
           <li>
-            <!-- JAL-3608 -->Options to allow user to choose the (Swing) Look and Feel used by Jalview
+            <!-- JAL-3608 -->Options to allow user to choose the (Swing) Look and Feel (LaF) used by Jalview
+          </li>
+          <li>
+            <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved operation on Linux Ubuntu with
+            HiDPI display in Java 11 (still known issues with HiDPI screens in java
+            8 and 11. see <a
+            href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
           </li>
           <li>
             <!-- JAL-3830 -->New command line launcher scripts (.sh, .ps1, .bat) usable on
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 4d1a453..e10c9eb 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -171,6 +171,8 @@ import jalview.ws.sifts.SiftsSettings;
  * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
  * respond to selections made in other alignments containing the same sequences.
  * </li>
+ * <li>SHOW_JWS2_SERVICES (true) when set to false, jalview will not
+ * auto-discover JABAWS services</li>
  * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
  * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
  * warning dialog box is displayed.</li>
@@ -198,7 +200,13 @@ import jalview.ws.sifts.SiftsSettings;
  * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
  * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
  * </li>
- * 
+ * <li>NONEWS - when set disables Jalview News from automatically appearing</li>
+ * <li>NOHTMLTEMPLATES - when set, the
+ * https://github.com/jalview/exporter-templates/tree/master/biojs repository is
+ * not downloaded automatically</li>
+ * <li>NOIDENTIFIERSSERVICE - when set, jalview won't automatically download
+ * available URL linkouts via www.jalview.org/services/identifiers</li>
+ * <li>
  * </ul>
  * Deprecated settings:
  * <ul>
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 4c018fb..357f0e4 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -475,12 +475,17 @@ public class Jalview
                   .println("CMD [-noquestionnaire] executed successfully!");
         }
 
-        if (!aparser.contains("nonews"))
+        if (!aparser.contains("nonews")
+                || Cache.getProperty("NONEWS") == null)
         {
           desktop.checkForNews();
         }
 
-        BioJsHTMLOutput.updateBioJS();
+        if (!aparser.contains("nohtmltemplates")
+              || Cache.getProperty("NOHTMLTEMPLATES") == null)
+        {
+          BioJsHTMLOutput.updateBioJS();
+        }
       }
     }
 
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 07baa2e..d791842 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4289,9 +4289,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   webService.add(me.webServiceNoServices);
                 }
                 // TODO: move into separate menu builder class.
-                boolean new_sspred = false;
-                if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
                 {
+                  // logic for 2.11.1.4 is
+                  // always look to see if there is a discover. if there isn't
+                  // we can't show any Jws2 services
+                  // if there are services available, show them - regardless of
+                  // the 'show JWS2 preference'
+                  // if the discoverer is running then say so
+                  // otherwise offer to trigger discovery if 'show JWS2' is not
+                  // enabled
                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
                   if (jws2servs != null)
                   {
@@ -4308,8 +4314,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                           }
                         }
                       }
-
                     }
+
                     if (jws2servs.isRunning())
                     {
                       JMenuItem tm = new JMenuItem(
@@ -4317,6 +4323,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       tm.setEnabled(false);
                       webService.add(tm);
                     }
+                    else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
+                    {
+                      JMenuItem enableJws2 = new JMenuItem(
+                              "Discover Web Services");
+                      enableJws2.setToolTipText(
+                              "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
+                      enableJws2.setEnabled(true);
+                      enableJws2.addActionListener(new ActionListener()
+                      {
+
+                        @Override
+                        public void actionPerformed(ActionEvent e)
+                        {
+                          // start service discoverer, but ignore preference
+                          Desktop.instance.startServiceDiscovery(false,
+                                  true);
+                        }
+                      });
+                      webService.add(enableJws2);
+                    }
                   }
                 }
                 build_urlServiceMenu(me.webService);
diff --git a/src/jalview/gui/BlogReader.java b/src/jalview/gui/BlogReader.java
index 3dc51ce..fb7d7c5 100644
--- a/src/jalview/gui/BlogReader.java
+++ b/src/jalview/gui/BlogReader.java
@@ -273,13 +273,16 @@ public class BlogReader extends JPanel
 
     initItems(chan);
     updating = false;
-    boolean setvisible = checkForNew(chan, true);
-
-    if (setvisible)
+    if (!Cache.getDefault("NONEWS", false))
     {
+      boolean setvisible = checkForNew(chan, true);
+
+      if (setvisible)
+      {
 
-      Console.debug("Will show jalview news automatically");
-      showNews();
+        Console.debug("Will show jalview news automatically");
+        showNews();
+      }
     }
     Console.debug("Completed construction of reader.");
 
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index c713a94..4f12de4 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -582,20 +582,28 @@ public class Desktop extends jalview.jbgui.GDesktop
     }).start();
   }
 
-  public void getIdentifiersOrgData() {
-    if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null) {
-      // Thread off the identifiers fetcher
-      new Thread(new Runnable() {
+  public void getIdentifiersOrgData()
+  {
+    if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null)
+    {// Thread off the identifiers fetcher
+      new Thread(new Runnable()
+      {
         @Override
-        public void run() {
+        public void run()
+        {
           jalview.bin.Console.debug("Downloading data from identifiers.org");
-          try {
-            UrlDownloadClient.download(IdOrgSettings.getUrl(), IdOrgSettings.getDownloadLocation());
-          } catch (IOException e) {
-            jalview.bin.Console.debug("Exception downloading identifiers.org data" + e.getMessage());
+          try
+          {
+            UrlDownloadClient.download(IdOrgSettings.getUrl(),
+                    IdOrgSettings.getDownloadLocation());
+          } catch (IOException e)
+          {
+            jalview.bin.Console.debug("Exception downloading identifiers.org data"
+                    + e.getMessage());
           }
         }
       }).start();
+      ;
     }
   }
 
@@ -2197,7 +2205,8 @@ public class Desktop extends jalview.jbgui.GDesktop
   /**
    * start service discovery and wait till it is done
    */
-  public void startServiceDiscovery() {
+  public void startServiceDiscovery()
+  {
     startServiceDiscovery(false);
   }
 
@@ -2206,8 +2215,9 @@ public class Desktop extends jalview.jbgui.GDesktop
    * 
    * @param blocking
    */
-  public void startServiceDiscovery(boolean blocking) {
-    startServiceDiscovery(blocking, false);
+  public void startServiceDiscovery(boolean blocking)
+  {
+    startServiceDiscovery(blocking,false);
   }
 
   /**
diff --git a/src/jalview/ws/utils/UrlDownloadClient.java b/src/jalview/ws/utils/UrlDownloadClient.java
index 58632f2..235d271 100644
--- a/src/jalview/ws/utils/UrlDownloadClient.java
+++ b/src/jalview/ws/utils/UrlDownloadClient.java
@@ -36,11 +36,6 @@ import java.nio.file.StandardCopyOption;
 
 public class UrlDownloadClient
 {
-  public UrlDownloadClient()
-  {
-
-  }
-
   /**
    * Download and save a file from a URL
    *