JAL-4409 JAL-4160 Don't let getdown turn jalviewX:// URIs into absolute local file...

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 90f627e..4e1fcab 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -281,11 +281,15 @@ 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);
       showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+      
+      showSSConsensus = Cache.getDefault("SHOW_SS_CONSENSUS", false);
 
       showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
     }
@@ -314,6 +318,7 @@ public class AlignViewport extends AlignmentViewport
     if (residueShading != null)
     {
       residueShading.setConsensus(hconsensus);
+      residueShading.setSsConsensus(hSSConsensus);
     }
     setColourAppliesToAllGroups(true);
   }
@@ -340,7 +345,7 @@ public class AlignViewport extends AlignmentViewport
     viewStyle.setFontName(font.getName());
     viewStyle.setFontStyle(font.getStyle());
     viewStyle.setFontSize(font.getSize());
-    
+
     validCharWidth = true;
   }
 
@@ -745,6 +750,11 @@ 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 +779,8 @@ 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 +814,10 @@ 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 +1002,7 @@ 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 +1163,5 @@ public class AlignViewport extends AlignmentViewport
   {
     this.viewName = viewName;
   }
+
 }