JAL-1619 refactoring in progress for Dna translation

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8ff9eda..cc7839e 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1122,7 +1122,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       currentFileFormat = chooser.getSelectedFormat();
-      if (currentFileFormat == null)
+      while (currentFileFormat == null)
       {
         JOptionPane
                 .showInternalMessageDialog(
@@ -1132,8 +1132,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         MessageManager
                                 .getString("label.file_format_not_specified"),
                         JOptionPane.WARNING_MESSAGE);
+        currentFileFormat = chooser.getSelectedFormat();
         value = chooser.showSaveDialog(this);
-        return;
+        if (value != JalviewFileChooser.APPROVE_OPTION)
+        {
+          return;
+        }
       }
 
       fileName = chooser.getSelectedFile().getPath();
@@ -4865,43 +4869,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
-  @Override
-  public void showProducts_actionPerformed(ActionEvent e)
-  {
-    // /////////////////////////////
-    // Collect Data to be translated/transferred
-
-    SequenceI[] selection = viewport.getSequenceSelection();
-    AlignmentI al = null;
-    try
-    {
-      al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
-              .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
-              viewport.getAlignment().getDataset());
-    } catch (Exception ex)
-    {
-      al = null;
-      jalview.bin.Cache.log.debug("Exception during translation.", ex);
-    }
-    if (al == null)
-    {
-      JOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
-                      MessageManager
-                              .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
-                      MessageManager.getString("label.translation_failed"),
-                      JOptionPane.WARNING_MESSAGE);
-    }
-    else
-    {
-      AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
-      Desktop.addInternalFrame(af, MessageManager.formatMessage(
-              "label.translation_of_params", new String[]
-              { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
-    }
-  }
-
   /**
    * Construct and display a new frame containing the translation of this
    * frame's cDNA sequences to their protein (amino acid) equivalents.
@@ -4917,7 +4884,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     AlignmentI al = null;
     try
     {
-      al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
+      al = jalview.analysis.Dna.cdnaTranslate(selection, seqstring,
               viewport.getViewAsVisibleContigs(true), viewport
                       .getGapCharacter(), viewport.getAlignment()
                       .getAlignmentAnnotation(), viewport.getAlignment()