X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=e9478d9fc1ac30ee7108ce5f96d9999b87d098d4;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=b492ddfb51ce34a60a066b6d9410d615ab9e246c;hpb=6dd554fdbf34db6b79595d5027159d20225f4894;p=jalview.git

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index b492ddf..e9478d9 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,15 +23,19 @@ 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;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.jbgui.GCutAndPasteTransfer;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
 
@@ -63,6 +67,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
   AlignViewportI viewport;
 
   FileParse source = null;
+
   public CutAndPasteTransfer()
   {
     SwingUtilities.invokeLater(new Runnable()
@@ -83,9 +88,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     this.alignpanel = viewpanel;
     if (alignpanel != null)
     {
-
+      this.viewport = alignpanel.getAlignViewport();
     }
-    this.viewport = alignpanel.getAlignViewport();
     if (viewport != null)
     {
       ok.setText(MessageManager.getString("action.add"));
@@ -127,7 +131,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
     chooser.setAcceptAllFileFilterUsed(false);
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.save_text_to_file"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.save_text_to_file"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
@@ -195,7 +200,27 @@ 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.
     AlignmentI al = null;
 
@@ -211,18 +236,17 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
       {
         JOptionPane.showInternalMessageDialog(Desktop.desktop,
                 MessageManager.formatMessage(
-                        "label.couldnt_read_pasted_text", new String[]
-                        { ex.toString() }), MessageManager
+                        "label.couldnt_read_pasted_text",
+                        new String[] { ex.toString() }), MessageManager
                         .getString("label.error_parsing_text"),
                 JOptionPane.WARNING_MESSAGE);
       }
     }
 
-    if (al != null)
+    if (al != null && al.hasValidSequence())
     {
       String title = MessageManager.formatMessage(
-              "label.input_cut_paste_params", new String[]
-              { format });
+              "label.input_cut_paste_params", new String[] { format });
       if (viewport != null)
       {
         ((AlignViewport) viewport).addAlignment(al, title);
@@ -239,13 +263,20 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
                   .getHiddenSequences();
           boolean showSeqFeatures = ((ComplexAlignFile) source)
                   .isShowSeqFeatures();
-          ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+          String colourSchemeName = ((ComplexAlignFile) source)
+                  .getGlobalColourScheme();
+          FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+                  .getDisplayedFeatures();
           af = new AlignFrame(al, hiddenSeqs, colSel,
-                  AlignFrame.DEFAULT_WIDTH,
-                  AlignFrame.DEFAULT_HEIGHT);
-
+                  AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
           af.getViewport().setShowSequenceFeatures(showSeqFeatures);
-          af.changeColour(cs);
+          af.getViewport().setFeaturesDisplayed(fd);
+          ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+                  colourSchemeName, al);
+          if (cs != null)
+          {
+            af.changeColour(cs);
+          }
         }
         else
         {
@@ -268,9 +299,20 @@ 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);
+      }
+    }
   }
 
-
   /**
    * DOCUMENT ME!
    *