JAL-1824 corrected copy'n'paste error introduced from JAL-1821 refactor which causes...

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

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 15e6818..cd5c792 100644 (file)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -23,9 +23,12 @@ package jalview.gui;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesDisplayedI;
+import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
 import jalview.io.FileParse;
 import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
@@ -58,7 +61,9 @@ import javax.swing.SwingUtilities;
 public class CutAndPasteTransfer extends GCutAndPasteTransfer
 {
 
-  AlignViewport viewport;
+  AlignmentViewPanel alignpanel;
+
+  AlignViewportI viewport;
 
   FileParse source = null;
   public CutAndPasteTransfer()
@@ -76,9 +81,13 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
   /**
    * DOCUMENT ME!
    */
-  public void setForInput(AlignViewport viewport)
+  public void setForInput(AlignmentViewPanel viewpanel)
   {
-    this.viewport = viewport;
+    this.alignpanel = viewpanel;
+    if (alignpanel != null)
+    {
+      this.viewport = alignpanel.getAlignViewport();
+    }
     if (viewport != null)
     {
       ok.setText(MessageManager.getString("action.add"));
@@ -188,15 +197,35 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
    */
   public void ok_actionPerformed(ActionEvent e)
   {
-    String format = new IdentifyFile().Identify(getText(), "Paste");
+    String text = getText();
+    if (text.trim().length() < 1)
+    {
+      return;
+    }
+
+    String format = new IdentifyFile().Identify(text, "Paste");
+    if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE"))
+    {
+      System.err.println(MessageManager
+              .getString("label.couldnt_read_data"));
+      if (!Jalview.isHeadlessMode())
+      {
+        javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                AppletFormatAdapter.SUPPORTED_FORMATS,
+                MessageManager.getString("label.couldnt_read_data"),
+                JOptionPane.WARNING_MESSAGE);
+      }
+      return;
+    }
+
     // TODO: identify feature, annotation or tree file and parse appropriately.
-    Alignment al = null;
+    AlignmentI al = null;
 
     if (FormatAdapter.isValidFormat(format))
     {
       try
       {
-        FormatAdapter fa = new FormatAdapter(viewport);
+        FormatAdapter fa = new FormatAdapter(alignpanel);
         al = fa.readFile(getText(), "Paste", format);
         source = fa.getAlignFile();
 
@@ -211,14 +240,14 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
       }
     }
 
-    if (al != null)
+    if (al != null && al.hasValidSequence())
     {
       String title = MessageManager.formatMessage(
               "label.input_cut_paste_params", new String[]
               { format });
       if (viewport != null)
       {
-        viewport.addAlignment(al, title);
+        ((AlignViewport) viewport).addAlignment(al, title);
       }
       else
       {
@@ -233,11 +262,13 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
           boolean showSeqFeatures = ((ComplexAlignFile) source)
                   .isShowSeqFeatures();
           ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+          FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+                  .getDisplayedFeatures();
           af = new AlignFrame(al, hiddenSeqs, colSel,
                   AlignFrame.DEFAULT_WIDTH,
                   AlignFrame.DEFAULT_HEIGHT);
-
           af.getViewport().setShowSequenceFeatures(showSeqFeatures);
+          af.getViewport().setFeaturesDisplayed(fd);
           af.changeColour(cs);
         }
         else
@@ -261,6 +292,18 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
         }
       }
     }
+    else
+    {
+      System.err.println(MessageManager
+              .getString("label.couldnt_read_data"));
+      if (!Jalview.isHeadlessMode())
+      {
+        javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                AppletFormatAdapter.SUPPORTED_FORMATS,
+                MessageManager.getString("label.couldnt_read_data"),
+                JOptionPane.WARNING_MESSAGE);
+      }
+    }
   }