JAL-3048 revised AlignExportSettings dialog with response action

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 1366ada..b764959 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -24,6 +24,7 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
 import jalview.api.AlignCalcManagerI;
+import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeaturesDisplayedI;
@@ -31,6 +32,7 @@ import jalview.api.ViewStyleI;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.Annotation;
@@ -2954,4 +2956,34 @@ public abstract class AlignmentViewport
   {
     return currentTree;
   }
+
+  @Override
+  public AlignmentExportData getAlignExportData(AlignExportSettingsI options)
+  {
+    AlignmentI alignmentToExport = null;
+    String[] omitHidden = null;
+    alignmentToExport = null;
+
+    if (hasHiddenColumns() && !options.isExportHiddenColumns())
+    {
+      omitHidden = getViewAsString(false,
+              options.isExportHiddenSequences());
+    }
+
+    int[] alignmentStartEnd = new int[2];
+    if (hasHiddenRows() && options.isExportHiddenSequences())
+    {
+      alignmentToExport = getAlignment().getHiddenSequences()
+              .getFullAlignment();
+    }
+    else
+    {
+      alignmentToExport = getAlignment();
+    }
+    alignmentStartEnd = getAlignment().getHiddenColumns()
+            .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
+    AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
+            omitHidden, alignmentStartEnd);
+    return ed;
+  }
 }