merge

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

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 6f15ddf..3d52ee1 100644 (file)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -20,17 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.Alignment;
-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.util.MessageManager;
-
 import java.awt.Toolkit;
 import java.awt.datatransfer.Clipboard;
 import java.awt.datatransfer.DataFlavor;
@@ -45,6 +34,19 @@ import javax.swing.JOptionPane;
 import javax.swing.JPopupMenu;
 import javax.swing.SwingUtilities;
 
+import jalview.api.ComplexAlignFile;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+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.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+
 /**
  * Cut'n'paste files into the desktop See JAL-1105
  * 
@@ -218,23 +220,49 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
       }
       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).applySettingsToAlignmentView(af);
+          ColumnSelection colSel = ((ComplexAlignFile) source)
+                  .getColumnSelection();
+          SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+                  .getHiddenSequences();
+          boolean showSeqFeatures = ((ComplexAlignFile) source)
+                  .isShowSeqFeatures();
+          ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+          af = new AlignFrame(al, hiddenSeqs, colSel,
+                  AlignFrame.DEFAULT_WIDTH,
+                  AlignFrame.DEFAULT_HEIGHT);
+
+          af.getViewport().setShowSequenceFeatures(showSeqFeatures);
+          af.changeColour(cs);
+          // ((HtmlFile) source).applySettingsToAlignmentView(af);
         }
-        else if (source instanceof JSONFile)
+        // else if (source instanceof JSONFile)
+        // {
+        // ColumnSelection colSel = ((JSONFile) source).getColumnSelection();
+        // SequenceI[] hiddenSeqs = ((JSONFile) source).getHiddenSequences();
+        // boolean showSeqFeatures = ((HtmlFile) source).isShowSeqFeatures();
+        // ColourSchemeI cs = ((HtmlFile) source).getColourScheme();
+        // af = new AlignFrame(al, hiddenSeqs, colSel,
+        // AlignFrame.DEFAULT_WIDTH,
+        // AlignFrame.DEFAULT_HEIGHT);
+        // af.getViewport().setShowSequenceFeatures(showSeqFeatures);
+        // af.changeColour(cs);
+        // // ((JSONFile) source).applySettingsToAlignmentView(af);
+        // }
+        else
         {
-          ((JSONFile) source).applySettingsToAlignmentView(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
         {