JAL-1780 improvement to ensure export settings dialog is not invoked if there's notin...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 14198b9..764b192 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -28,7 +28,6 @@ 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;
@@ -306,7 +305,6 @@ 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 +1140,7 @@ 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 +1221,8 @@ 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(),
@@ -1254,7 +1253,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     { 0, alignmentToExport.getWidth() - 1 };
 
     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
-    AlignExportSettingI settings = new AlignExportSettings(hasHiddenSeqs,
+    AlignExportSettings settings = new AlignExportSettings(hasHiddenSeqs,
             viewport.hasHiddenColumns(), exportFomat);
     settings.isExportAnnotations();
 
@@ -6079,10 +6078,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     private int[] startEnd;
 
-    private AlignExportSettingI settings;
+    private AlignExportSettings settings;
 
     public ExportData(AlignmentI align, String[] ommit, int[] startEnd,
-            AlignExportSettingI settings)
+            AlignExportSettings settings)
     {
       this.alignment = align;
       this.omitHidden = ommit;
@@ -6120,12 +6119,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       this.startEnd = startEnd;
     }
 
-    public AlignExportSettingI getSettings()
+    public AlignExportSettings getSettings()
     {
       return settings;
     }
 
-    public void setSettings(AlignExportSettingI settings)
+    public void setSettings(AlignExportSettings settings)
     {
       this.settings = settings;
     }