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 3b1b147..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);
   }
@@ -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)
@@ -801,27 +812,12 @@ public class AlignViewport extends AlignmentViewport
      * in reverse order)
      */
     JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
-            .setResponseHandler(0, new Runnable()
-            {
-              @Override
-              public void run()
-              {
-                addDataToAlignment(al);
-              }
-            }).setResponseHandler(1, new Runnable()
-            {
-              @Override
-              public void run()
-              {
-                us.openLinkedAlignmentAs(al, title, true);
-              }
-            }).setResponseHandler(2, new Runnable()
-            {
-              @Override
-              public void run()
-              {
-                us.openLinkedAlignmentAs(al, title, false);
-              }
+            .setResponseHandler(0, () -> {
+              addDataToAlignment(al);
+            }).setResponseHandler(1, () -> {
+              us.openLinkedAlignmentAs(al, title, true);
+            }).setResponseHandler(2, () -> {
+              us.openLinkedAlignmentAs(al, title, false);
             });
     dialog.showDialog(question,
             MessageManager.getString("label.open_split_window"),
@@ -1006,7 +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;
@@ -1167,4 +1163,5 @@ public class AlignViewport extends AlignmentViewport
   {
     this.viewName = viewName;
   }
+
 }