JAL-1780 more support for export setting for flatfile output

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index db61f77..85b6767 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -74,6 +74,7 @@ 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;
@@ -1140,7 +1141,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         return false;
       }
 
-      ExportData exportData = getAlignmentForExport();
+      ExportData exportData = getAlignmentForExport(format);
       FormatAdapter f = new FormatAdapter(viewport);
       String output = f.formatSequences(format,
               exportData.getAlignment(), // class cast exceptions will
@@ -1213,10 +1214,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void outputText_actionPerformed(ActionEvent e)
   {
 
-    ExportData exportData = getAlignmentForExport();
+    ExportData exportData = getAlignmentForExport(e.getActionCommand());
+    if (exportData.getSettings().isCancelled())
+    {
+      return;
+    }
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(null);
-
     try
     {
       cap.setText(new FormatAdapter(viewport).formatSequences(
@@ -1235,7 +1239,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   }
 
-  public ExportData getAlignmentForExport()
+  public ExportData getAlignmentForExport(String exportFomat)
   {
     AlignmentI alignmentToExport = null;
     String[] omitHidden = null;
@@ -1250,36 +1254,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignmentStartEnd = new int[]
     { 0, alignmentToExport.getWidth() - 1 };
 
-    if (viewport.hasHiddenColumns() || hiddenSeqs.getSize() > 0)
-    {
-      int reply = JOptionPane
-              .showInternalConfirmDialog(
-                      Desktop.desktop,
-                      MessageManager
-                              .getString("label.alignment_contains_hidden_columns"),
-                      MessageManager
-                              .getString("action.save_omit_hidden_columns"),
-                      JOptionPane.YES_NO_OPTION,
-                      JOptionPane.QUESTION_MESSAGE);
+    boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
+    AlignExportSettingI settings = new AlignExportSettings(hasHiddenSeqs,
+            viewport.hasHiddenColumns(), exportFomat);
+    viewport.setExportSettings(settings);
+    settings.isExportAnnotations();
 
-      if (reply == JOptionPane.YES_OPTION)
-      {
-        // export only visible region
-        omitHidden = viewport.getViewAsString(false);
-        alignmentToExport = viewport.getAlignment();
-        alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
-                .getColumnSelection().getHiddenColumns());
-        viewport.setIncludeHiddenRegion(false);
-      }
-      else
-      {
-        // export all region including visible
-        alignmentToExport = hiddenSeqs.getFullAlignment();
-        viewport.setIncludeHiddenRegion(true);
-      }
+    if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
+    {
+      omitHidden = viewport.getViewAsString(false);
     }
 
-    return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd);
+    if (hasHiddenSeqs && settings.isExportHiddenSequences())
+    {
+      alignmentToExport = hiddenSeqs.getFullAlignment();
+    }
+    else
+    {
+      alignmentToExport = viewport.getAlignment();
+      alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
+              .getColumnSelection().getHiddenColumns());
+    }
+    return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd,
+            settings);
   }
 
   private static int[] getStartEnd(int[] aligmentStartEnd,
@@ -1352,9 +1349,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    // new HTMLOutput(alignPanel,
-    // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
-    // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
     new HtmlSvgOutput(null, alignPanel);
   }
 
@@ -6094,11 +6088,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     private int[] startEnd;
 
-    public ExportData(AlignmentI align, String[] ommit, int[] startEnd)
+    private AlignExportSettingI settings;
+
+    public ExportData(AlignmentI align, String[] ommit, int[] startEnd,
+            AlignExportSettingI settings)
     {
       this.alignment = align;
       this.omitHidden = ommit;
       this.startEnd = startEnd;
+      this.settings = settings;
     }
 
     public AlignmentI getAlignment()
@@ -6130,6 +6128,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       this.startEnd = startEnd;
     }
+
+    public AlignExportSettingI getSettings()
+    {
+      return settings;
+    }
+
+    public void setSettings(AlignExportSettingI settings)
+    {
+      this.settings = settings;
+    }
   }
 
 }