another merge from develop

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bdcf8a4..809609a 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -28,6 +28,7 @@ import jalview.analysis.CrossRef;
 import jalview.analysis.Dna;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignExportSettingI;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
@@ -1147,7 +1148,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         return false;
       }
 
-      AlignmentExportData exportData = getAlignmentForExport(format, viewport);
+      AlignmentExportData exportData = getAlignmentForExport(format,
+              viewport, null);
       if (exportData.getSettings().isCancelled())
       {
         return false;
@@ -1226,7 +1228,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
 
     AlignmentExportData exportData = getAlignmentForExport(
-            e.getActionCommand(), viewport);
+            e.getActionCommand(), viewport, null);
     if (exportData.getSettings().isCancelled())
     {
       return;
@@ -1253,9 +1255,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   public static AlignmentExportData getAlignmentForExport(String exportFormat,
-          AlignViewportI viewport)
+ AlignViewportI viewport,
+          AlignExportSettingI exportSettings)
   {
     AlignmentI alignmentToExport = null;
+    AlignExportSettingI settings = exportSettings;
     String[] omitHidden = null;
     int[] alignmentStartEnd = new int[2];
 
@@ -1268,9 +1272,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     { 0, alignmentToExport.getWidth() - 1 };
 
     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
-    AlignExportSettings settings = new AlignExportSettings(hasHiddenSeqs,
+    if (settings == null)
+    {
+      settings = new AlignExportSettings(hasHiddenSeqs,
             viewport.hasHiddenColumns(), exportFormat);
-    settings.isExportAnnotations();
+    }
+    // settings.isExportAnnotations();
 
     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
     {