JAL-1641 refactor

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8462b8d..db61f77 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -240,6 +240,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     this(al, hiddenColumns, width, height, null);
   }
 
+
   /**
    * Create alignment frame for al with hiddenColumns, a specific width and
    * height, and specific sequenceId
@@ -289,6 +290,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     init();
   }
 
+  public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+          ColumnSelection hiddenColumns, int width, int height)
+  {
+    setSize(width, height);
+
+    if (al.getDataset() == null)
+    {
+      al.setDataset(null);
+    }
+
+    viewport = new AlignViewport(al, hiddenColumns);
+
+    if (hiddenSeqs != null && hiddenSeqs.length > 0)
+    {
+      viewport.hideSequence(hiddenSeqs);
+      viewport.setHasHiddenRows(true);
+    }
+    alignPanel = new AlignmentPanel(this, viewport);
+    addAlignmentPanel(alignPanel, true);
+    init();
+  }
+
+
   /**
    * Make a new AlignFrame from existing alignmentPanels
    * 
@@ -6108,33 +6132,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
-  @Override
-  public void hideColumns(List<int[]> colsToHide)
-  {
-    for (int[] colRange : colsToHide)
-    {
-      viewport.hideColumns(colRange[0], colRange[1]);
-    }
-
-  }
-
-  @Override
-  public void syncHiddenSequences()
-  {
-    AlignmentI al = viewport.getAlignment();
-    HiddenSequences hiddenSeqs = al.getHiddenSequences();
-    boolean hasHiddenRows = false;
-    for (SequenceI seq : al.getSequencesArray())
-      {
-        if (seq.isHidden())
-        {
-        hiddenSeqs.hideSequence(seq);
-        hasHiddenRows = true;
-        }
-      }
-    viewport.setHasHiddenRows(hasHiddenRows);
-    firePropertyChange("alignment", null, al.getSequences());
-  }
 }
 
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