JAL-1619 split frame now offered in applet 'input from textbox'

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 3499fdd..6f47422 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1196,11 +1196,12 @@ label.show_logo = Show Logo
 label.normalise_logo = Normalise Logo
 label.no_colour_selection_in_scheme = Please, make a colour selection before to apply colour scheme
 label.no_colour_selection_warn = Error saving colour scheme
-label.open_linked_alignment? = Would you like to open as a separate alignment, with cDNA and protein linked?
-label.open_linked_alignment = Open linked alignment
+label.open_split_window? = Would you like to open as a split window, with cDNA and protein linked?
+label.open_split_window = Open split window
 label.no_mappings = No mappings found
 label.mapping_failed = No sequence mapping could be made between the alignments.<br>A mapping requires sequence names to match, and equivalent sequence lengths.
 action.no = No
+action.yes = Yes
 label.for = for
 label.select_by_annotation = Select By Annotation
 action.select_by_annotation = Select by Annotation...

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index cd6c9e5..dc4539e 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1217,7 +1217,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
-            "label.alignment_output_command", new String[]
+            "label.alignment_output_command", new Object[]
             { e.getActionCommand() }), 600, 500);
     cap.setText(new AppletFormatAdapter().formatSequences(
             e.getActionCommand(), viewport.getAlignment(),

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 0c717b2..248153f 100644 (file)
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -20,7 +20,11 @@
  */
 package jalview.appletgui;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.AlignmentUtils.MappingResult;
+import jalview.bin.JalviewLite;
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.io.AnnotationFile;
@@ -36,6 +40,7 @@ import java.awt.Button;
 import java.awt.Dialog;
 import java.awt.Font;
 import java.awt.Frame;
+import java.awt.Label;
 import java.awt.Panel;
 import java.awt.TextArea;
 import java.awt.event.ActionEvent;
@@ -225,7 +230,11 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
     if (al != null)
     {
-      al.setDataset(null);
+      al.setDataset(null); // set dataset on alignment/sequences
+      if (openSplitFrame(al, format))
+      {
+        return;
+      }
       if (newWindow)
       {
         AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
@@ -244,6 +253,69 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
   }
 
   /**
+   * Check whether the new alignment could be mapped to the current one as
+   * cDNA/protein, if so offer the option to open as split frame view. Returns
+   * true if a split frame view is opened, false if not.
+   * 
+   * @param al
+   * @return
+   */
+  protected boolean openSplitFrame(Alignment al, String format)
+  {
+    final AlignmentI thisAlignment = this.alignFrame.getAlignViewport().getAlignment();
+    if (thisAlignment.isNucleotide() == al.isNucleotide())
+    {
+      // both nucleotide or both protein
+      return false;
+    }
+    AlignmentI protein = thisAlignment.isNucleotide() ? al : thisAlignment;
+    AlignmentI dna = thisAlignment.isNucleotide() ? thisAlignment : al;
+    MappingResult mapped = AlignmentUtils.mapProteinToCdna(protein, dna);
+    if (mapped == MappingResult.NotMapped)
+    {
+      return false;
+    }
+
+    /*
+     * A mapping is possible; ask user if they want a split frame.
+     */
+    String title = MessageManager.getString("label.open_split_window");
+    final JVDialog dialog = new JVDialog((Frame) this.getParent(), title,
+            true, 100, 400);
+    dialog.ok.setLabel(MessageManager.getString("action.yes"));
+    dialog.cancel.setLabel(MessageManager.getString("action.no"));
+    Panel question = new Panel(new BorderLayout());
+    final String text = MessageManager
+            .getString("label.open_split_window?");
+    question.add(new Label(text, Label.CENTER), BorderLayout.CENTER);
+    dialog.setMainPanel(question);
+    dialog.setVisible(true);
+    dialog.toFront();
+    
+    if (!dialog.accept)
+    {
+      return false;
+    }
+
+    /*
+     * Open SplitFrame with DNA above and protein below, including the alignment
+     * from textbox and a copy of the original.
+     */
+    final JalviewLite applet = this.alignFrame.viewport.applet;
+    AlignFrame copyFrame = new AlignFrame(
+            this.alignFrame.viewport.getAlignment(), applet,
+            alignFrame.getTitle(), false, false);
+    AlignFrame newFrame = new AlignFrame(al, alignFrame.viewport.applet,
+            "Cut & Paste input - " + format, false, false);
+    AlignFrame dnaFrame = al.isNucleotide() ? newFrame : copyFrame;
+    AlignFrame proteinFrame = al.isNucleotide() ? copyFrame
+            : newFrame;
+    SplitFrame sf = new SplitFrame(dnaFrame, proteinFrame);
+    sf.addToDisplay(false, applet);
+    return true;
+  }
+
+  /**
    * Parse the text as a TCoffee score file, if successful add scores as
    * alignment annotations.
    */

diff --git a/src/jalview/appletgui/SplitFrame.java b/src/jalview/appletgui/SplitFrame.java
index a012092..4f61f4a 100644 (file)
--- a/src/jalview/appletgui/SplitFrame.java
+++ b/src/jalview/appletgui/SplitFrame.java
@@ -40,8 +40,7 @@ public class SplitFrame extends EmbmenuFrame
   public void init()
   {
     setMenuBar(null);
-    outermost = new Panel();
-    outermost.setLayout(new GridLayout(2, 1));
+    outermost = new Panel(new GridLayout(2, 1));
 
     Panel topPanel = new Panel();
     Panel bottomPanel = new Panel();
@@ -58,12 +57,11 @@ public class SplitFrame extends EmbmenuFrame
     final AlignViewport bottomViewport = bottomFrame.viewport;
     final AlignmentI topAlignment = topViewport.getAlignment();
     final AlignmentI bottomAlignment = bottomViewport.getAlignment();
-    // topAlignment.setDataset(null);
-    // bottomAlignment.setDataset(null);
     AlignViewport cdna = topAlignment.isNucleotide() ? topViewport
             : (bottomAlignment.isNucleotide() ? bottomViewport : null);
     AlignViewport protein = !topAlignment.isNucleotide() ? topViewport
             : (!bottomAlignment.isNucleotide() ? bottomViewport : null);
+
     MappingResult mapped = AlignmentUtils.mapProteinToCdna(
             protein.getAlignment(), cdna.getAlignment());
     if (mapped != MappingResult.NotMapped)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 8fc10d7..2129db1 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -977,9 +977,9 @@ public class AlignViewport extends AlignmentViewport implements
         MessageManager.getString("label.split_window"),
         MessageManager.getString("label.new_window"), };
     final String question = JvSwingUtils.wrapTooltip(true,
-            MessageManager.getString("label.open_linked_alignment?"));
+            MessageManager.getString("label.open_split_window?"));
     int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
-            MessageManager.getString("label.open_linked_alignment"),
+            MessageManager.getString("label.open_split_window"),
             JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
             options, options[0]);