X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=037f1201171e9390816e53a28da6906082c5362d;hb=b254ce17e47c43d19804efa129367291a79b1315;hp=fea74db0ce48d12520463f6772638f8b1d854a22;hpb=0de37d1a047209510bab82225109ae2a47931f79;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index fea74db..037f120 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -281,7 +281,9 @@ public class AlignViewport extends AlignmentViewport
       }
       showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
               true);
-      showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
+      showSSConsensusHistogram = Cache.getDefault("SHOW_SSCONSENSUS_HISTOGRAM",
+              true);
+      showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", true);
       normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
               false);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
@@ -314,6 +316,7 @@ public class AlignViewport extends AlignmentViewport
     if (residueShading != null)
     {
       residueShading.setConsensus(hconsensus);
+      residueShading.setSsConsensus(hSSConsensus);
     }
     setColourAppliesToAllGroups(true);
   }
@@ -745,6 +748,11 @@ public class AlignViewport extends AlignmentViewport
    */
   public void addFile(File file, FileFormatI format)
   {
+    addFile(file, format, true);
+  }
+
+  public void addFile(File file, FileFormatI format, boolean async)
+  {
     DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
 
     if (format == null)
@@ -769,7 +777,8 @@ public class AlignViewport extends AlignmentViewport
       }
     }
 
-    new FileLoader().LoadFile(this, file, DataSourceType.FILE, format);
+    new FileLoader().LoadFile(this, file, DataSourceType.FILE, format,
+            async);
   }
 
   public void addFile(File file)
@@ -803,13 +812,10 @@ public class AlignViewport extends AlignmentViewport
     JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
             .setResponseHandler(0, () -> {
               addDataToAlignment(al);
-              return null;
             }).setResponseHandler(1, () -> {
               us.openLinkedAlignmentAs(al, title, true);
-              return null;
             }).setResponseHandler(2, () -> {
               us.openLinkedAlignmentAs(al, title, false);
-              return null;
             });
     dialog.showDialog(question,
             MessageManager.getString("label.open_split_window"),
@@ -994,7 +1000,7 @@ public class AlignViewport extends AlignmentViewport
    */
   protected boolean noReferencesTo(AlignedCodonFrame acf)
   {
-    AlignFrame[] frames = Desktop.getAlignFrames();
+    AlignFrame[] frames = Desktop.getDesktopAlignFrames();
     if (frames == null)
     {
       return true;
@@ -1155,4 +1161,5 @@ public class AlignViewport extends AlignmentViewport
   {
     this.viewName = viewName;
   }
+
 }