JAL-1619 refactoring wip

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 7a36754..5fe97a4 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -25,6 +25,7 @@ import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
 import jalview.analysis.CrossRef;
+import jalview.analysis.Dna;
 import jalview.analysis.NJTree;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
@@ -797,7 +798,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           seqCount += seqsAligned;
           if (seqsAligned > 0)
           {
-            af.viewport.alignmentChanged(af.alignPanel);
+            af.alignPanel.alignmentChanged();
             alignCount++;
           }
         }
@@ -1122,7 +1123,7 @@ 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 +1133,12 @@ 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();
@@ -4865,89 +4870,40 @@ 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.
+   * frame's cDNA sequences to their aligned protein (amino acid) equivalents.
    */
   @Override
   public void showTranslation_actionPerformed(ActionEvent e)
   {
-    // /////////////////////////////
-    // Collect Data to be translated/transferred
-
-    SequenceI[] selection = viewport.getSequenceSelection();
-    String[] seqstring = viewport.getViewAsString(true);
     AlignmentI al = null;
     try
     {
-      al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
-              viewport.getViewAsVisibleContigs(true), viewport
-                      .getGapCharacter(), viewport.getAlignment()
-                      .getAlignmentAnnotation(), viewport.getAlignment()
-                      .getWidth(), viewport.getAlignment().getDataset());
+      Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
+
+      al = dna.translateCdna();
     } catch (Exception ex)
     {
-      al = null;
       jalview.bin.Cache.log.error(
               "Exception during translation. Please report this !", ex);
-      JOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
-                      MessageManager
-                              .getString("label.error_when_translating_sequences_submit_bug_report"),
-                      MessageManager
-                              .getString("label.implementation_error")
-                              + MessageManager
-                                      .getString("translation_failed"),
-                      JOptionPane.ERROR_MESSAGE);
+      final String msg = MessageManager
+              .getString("label.error_when_translating_sequences_submit_bug_report");
+      final String title = MessageManager
+              .getString("label.implementation_error")
+              + MessageManager.getString("translation_failed");
+      JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+              JOptionPane.ERROR_MESSAGE);
       return;
     }
     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);
+      final String msg = MessageManager
+              .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
+      final String title = MessageManager
+              .getString("label.translation_failed");
+      JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+              JOptionPane.WARNING_MESSAGE);
     }
     else
     {