JAl-1705 ENSEMBL cDNA type cannot be queried with peptide IDs

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 14198b9..01353d8 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -306,7 +306,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (hiddenSeqs != null && hiddenSeqs.length > 0)
     {
       viewport.hideSequence(hiddenSeqs);
-      viewport.setHasHiddenRows(true);
     }
     alignPanel = new AlignmentPanel(this, viewport);
     addAlignmentPanel(alignPanel, true);
@@ -1142,7 +1141,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
 
       ExportData exportData = getAlignmentForExport(format);
-      FormatAdapter f = new FormatAdapter(viewport);
+      FormatAdapter f = new FormatAdapter(alignPanel);
       String output = f.formatSequences(format,
               exportData.getAlignment(), // class cast exceptions will
               // occur in the distant future
@@ -1223,7 +1222,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     cap.setForInput(null);
     try
     {
-      cap.setText(new FormatAdapter(viewport).formatSequences(
+      cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
+              .formatSequences(
               e.getActionCommand(),
  exportData.getAlignment(),
               exportData.getOmitHidden(), exportData.getStartEndPostions(),