X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=979d1aa0f4b274e2a286028d34efd292918e714f;hb=f0abe70b5a54b6a9730aa5f4e2bf2bd697508757;hp=19814882b784438b1905acbb0931adcd6d722254;hpb=7ce1382b998c007a78c9b33a3dc331e966eebc4b;p=jalview.git

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 1981488..979d1aa 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -20,15 +20,20 @@
  */
 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.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
 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;
@@ -54,7 +59,9 @@ import javax.swing.SwingUtilities;
 public class CutAndPasteTransfer extends GCutAndPasteTransfer
 {
 
-  AlignViewport viewport;
+  AlignmentViewPanel alignpanel;
+
+  AlignViewportI viewport;
 
   FileParse source = null;
   public CutAndPasteTransfer()
@@ -72,9 +79,13 @@ 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"));
@@ -184,15 +195,21 @@ 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");
     // 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();
 
@@ -214,27 +231,41 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
               { 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).applySettingsToAlignFrame(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).applySettingsToAlignFrame(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
         {