Merge branch 'develop' into Release_2_9_Branch

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

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 3f4aa71..9c5651a 100644 (file)
--- 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)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,15 +20,22 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.Alignment;
+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.HtmlFile;
 import jalview.io.IdentifyFile;
-import jalview.io.JSONFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.jbgui.GCutAndPasteTransfer;
+import jalview.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
 
 import java.awt.Toolkit;
@@ -54,9 +61,12 @@ import javax.swing.SwingUtilities;
 public class CutAndPasteTransfer extends GCutAndPasteTransfer
 {
 
-  AlignViewport viewport;
+  AlignmentViewPanel alignpanel;
+
+  AlignViewportI viewport;
 
   FileParse source = null;
+
   public CutAndPasteTransfer()
   {
     SwingUtilities.invokeLater(new Runnable()
@@ -72,9 +82,13 @@ 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"));
@@ -116,7 +130,8 @@ 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);
@@ -184,15 +199,35 @@ 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();
 
@@ -200,41 +235,53 @@ 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)
       {
-        viewport.addAlignment(al, title);
+        ((AlignViewport) viewport).addAlignment(al, title);
       }
       else
       {
-        AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
-                AlignFrame.DEFAULT_HEIGHT);
-        af.currentFileFormat = format;
-        Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
-                AlignFrame.DEFAULT_HEIGHT);
-        af.statusBar.setText(MessageManager
-                .getString("label.successfully_pasted_alignment_file"));
 
-        if (source instanceof HtmlFile)
+        AlignFrame af;
+        if (source instanceof ComplexAlignFile)
         {
-          ((HtmlFile) source).LoadAlignmentFeatures(af);
+          ColumnSelection colSel = ((ComplexAlignFile) source)
+                  .getColumnSelection();
+          SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+                  .getHiddenSequences();
+          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 if (source instanceof JSONFile)
+        else
         {
-          ((JSONFile) source).LoadAlignmentFeatures(af);
+          af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+                  AlignFrame.DEFAULT_HEIGHT);
         }
 
+        af.currentFileFormat = format;
+        Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
+                AlignFrame.DEFAULT_HEIGHT);
+        af.statusBar.setText(MessageManager
+                .getString("label.successfully_pasted_alignment_file"));
 
         try
         {
@@ -245,9 +292,20 @@ 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!
    *