JAL-1641 refactor

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 1b1a5b8..1510a14 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -156,6 +156,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public AlignFrame(AlignmentI al, JalviewLite applet,
           String title, boolean embedded, boolean addToDisplay)
   {
+    this(al, null, null, applet, title, embedded, addToDisplay);
+  }
+
+  public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+          ColumnSelection columnSelection, JalviewLite applet,
+          String title, boolean embedded)
+  {
+    this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
+  }
+
+  public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+          ColumnSelection columnSelection, JalviewLite applet,
+          String title, boolean embedded, boolean addToDisplay)
+  {
     if (applet != null)
     {
       jalviewServletURL = applet.getParameter("APPLICATION_URL");
@@ -191,6 +205,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
     }
     viewport = new AlignViewport(al, applet);
+
+    if (hiddenSeqs != null && hiddenSeqs.length > 0)
+    {
+      viewport.hideSequence(hiddenSeqs);
+      viewport.setHasHiddenRows(true);
+    }
+    if (columnSelection != null)
+    {
+      viewport.setColumnSelection(columnSelection);
+    }
+
     alignPanel = new AlignmentPanel(this, viewport);
     avc = new jalview.controller.AlignViewController(this, viewport,
             alignPanel);
@@ -4182,32 +4207,4 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     this.splitFrame = sf;
   }
-
-  @Override
-  public void setShowSeqFeatures(boolean b)
-  {
-    this.sequenceFeatures.setState(b);
-    viewport.setShowSequenceFeatures(b);
-  }
-
-  @Override
-  public void setMenusForViewport()
-  {
-    // setMenusFromViewport(viewport);
-
-  }
-
-  @Override
-  public void hideColumns(List<int[]> colsToHide)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public void syncHiddenSequences()
-  {
-    // TODO Auto-generated method stub
-
-  }
 }