X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=db61f77f0ebbb7362f4cf5a8f713575c456be6ba;hb=70f9c4700f20a8fa57ed7eb974277d8bad0723c2;hp=64818559caf57c3dfc134916a00ac298aa9a51d7;hpb=d7989f319488cc56440f822261bc5014c27e03c6;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 6481855..db61f77 100644
--- 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
    * 
@@ -1098,11 +1122,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 .lastIndexOf(java.io.File.separatorChar) + 1);
       }
 
-      /*
-       * First save any linked Chimera session.
-       */
-      Desktop.instance.saveChimeraSessions(file);
-
       success = new Jalview2XML().saveAlignment(this, file, shortName);
 
       statusBar.setText(MessageManager.formatMessage(
@@ -1250,11 +1269,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         alignmentToExport = viewport.getAlignment();
         alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
                 .getColumnSelection().getHiddenColumns());
+        viewport.setIncludeHiddenRegion(false);
       }
       else
       {
         // export all region including visible
         alignmentToExport = hiddenSeqs.getFullAlignment();
+        viewport.setIncludeHiddenRegion(true);
       }
     }
 
@@ -6111,29 +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();
-    for (SequenceI seq : al.getSequencesArray())
-      {
-        if (seq.isHidden())
-        {
-        hiddenSeqs.hideSequence(seq);
-        }
-      }
-  }
 }
 
 class PrintThread extends Thread