Copy and paste of annotations with seqrefs

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a73958d..151eb5e 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -44,7 +44,7 @@ import java.awt.dnd.*;
  * @version $Revision$\r
  */\r
 public class AlignFrame\r
-    extends GAlignFrame implements ClipboardOwner, DropTargetListener\r
+    extends GAlignFrame implements DropTargetListener\r
 {\r
   /** DOCUMENT ME!! */\r
   public static final int NEW_WINDOW_WIDTH = 700;\r
@@ -542,10 +542,6 @@ public class AlignFrame
     alignPanel.repaint();\r
   }\r
 \r
-  public void lostOwnership(Clipboard clipboard, Transferable contents)\r
-  {\r
-    Desktop.jalviewClipboard = null;\r
-  }\r
 \r
 \r
   /**\r
@@ -626,12 +622,16 @@ public class AlignFrame
       seqs[i].setDBRef(seq.getDBRef());\r
       seqs[i].setSequenceFeatures(seq.getSequenceFeatures());\r
       seqs[i].setDatasetSequence(seq.getDatasetSequence());\r
-\r
+      if(seq.getAnnotation()!=null)\r
+      {\r
+        for(int a=0; a<seq.getAnnotation().length; a++)\r
+          seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);\r
+      }\r
     }\r
 \r
     FastaFile ff = new FastaFile();\r
     ff.addJVSuffix( viewport.showJVSuffix );\r
-    c.setContents(new StringSelection( ff.print(seqs)), this);\r
+    c.setContents(new StringSelection( ff.print(seqs)), Desktop.instance);\r
     Desktop.jalviewClipboard = new Object[]{seqs,  viewport.alignment.getDataset()};\r
   }\r
 \r
@@ -692,46 +692,30 @@ public class AlignFrame
        sequences = new FormatAdapter().readFile(str, "Paste", format);\r
      }\r
 \r
+     AlignmentI alignment = null;\r
+\r
       if (newAlignment)\r
       {\r
-\r
-        Alignment alignment = new Alignment(sequences);\r
+        alignment = new Alignment(sequences);\r
 \r
         if(Desktop.jalviewClipboard!=null)\r
            alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );\r
         else\r
            alignment.setDataset( null );\r
-\r
-\r
-        AlignFrame af = new AlignFrame(alignment);\r
-        String newtitle = new String("Copied sequences");\r
-\r
-        //>>>This is a fix for the moment, until a better solution is found!!<<<\r
-        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(\r
-            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
-\r
-\r
-        if (title.startsWith("Copied sequences"))\r
-        {\r
-          newtitle = title;\r
-        }\r
-        else\r
-        {\r
-          newtitle = newtitle.concat("- from " + title);\r
-        }\r
-\r
-        Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
-                                 NEW_WINDOW_HEIGHT);\r
       }\r
       else\r
       {\r
+        alignment = viewport.getAlignment();\r
+\r
         //!newAlignment\r
         for (int i = 0; i < sequences.length; i++)\r
         {\r
+\r
           Sequence newseq = new Sequence(sequences[i].getName(),\r
               sequences[i].getSequence(), sequences[i].getStart(),\r
               sequences[i].getEnd());\r
-          viewport.alignment.addSequence(newseq);\r
+\r
+          alignment.addSequence(newseq);\r
           if(sequences[i].getDatasetSequence()==null)\r
           {\r
              ////////////////////////////\r
@@ -742,24 +726,73 @@ public class AlignFrame
                                        sequences[i].getStart(),\r
                                        sequences[i].getEnd());\r
             newseq.setDatasetSequence(ds);\r
-            viewport.alignment.getDataset().addSequence(ds);\r
+            alignment.getDataset().addSequence(ds);\r
           }\r
           else\r
           {\r
             newseq.setDatasetSequence(sequences[i].getDatasetSequence());\r
-            if(sequences[i].getDatasetSequence().getAnnotation()!=null)\r
-            {\r
-              for(int aa=0; aa<sequences[i].getDatasetSequence().getAnnotation().length; aa++)\r
-              {\r
-                viewport.alignment.addAnnotation(sequences[i].getDatasetSequence().getAnnotation()[aa]);\r
-              }\r
-            }\r
           }\r
         }\r
-        viewport.setEndSeq(viewport.alignment.getHeight());\r
-        viewport.alignment.getWidth();\r
-        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+        viewport.setEndSeq(alignment.getHeight());\r
+        alignment.getWidth();\r
+        viewport.firePropertyChange("alignment", null, alignment.getSequences());\r
       }\r
+\r
+      // Add any annotations attached to sequences\r
+      for (int i = 0; i < sequences.length; i++)\r
+     {\r
+       if (sequences[i].getAnnotation() != null)\r
+       {\r
+         for (int a = 0; a < sequences[i].getAnnotation().length; a++)\r
+         {\r
+           AlignmentAnnotation newAnnot =\r
+               new AlignmentAnnotation(\r
+                   sequences[i].getAnnotation()[a].label,\r
+                   sequences[i].getAnnotation()[a].description,\r
+                   sequences[i].getAnnotation()[a].annotations,\r
+                   sequences[i].getAnnotation()[a].graphMin,\r
+                   sequences[i].getAnnotation()[a].graphMax,\r
+                   sequences[i].getAnnotation()[a].graph);\r
+\r
+           sequences[i].getAnnotation()[a] = newAnnot;\r
+           newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].\r
+               sequenceMapping;\r
+           newAnnot.sequenceRef = sequences[i];\r
+           newAnnot.adjustForAlignment();\r
+           alignment.addAnnotation(newAnnot);\r
+           alignment.setAnnotationIndex(newAnnot, a);\r
+         }\r
+\r
+         alignPanel.annotationPanel.adjustPanelHeight();\r
+       }\r
+     }\r
+\r
+     if(newAlignment)\r
+     {\r
+       AlignFrame af = new AlignFrame(alignment);\r
+       String newtitle = new String("Copied sequences");\r
+\r
+\r
+       //>>>This is a fix for the moment, until a better solution is found!!<<<\r
+       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(\r
+           alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
+\r
+\r
+       if (title.startsWith("Copied sequences"))\r
+       {\r
+         newtitle = title;\r
+       }\r
+       else\r
+       {\r
+         newtitle = newtitle.concat("- from " + title);\r
+       }\r
+\r
+       Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
+                                NEW_WINDOW_HEIGHT);\r
+\r
+     }\r
+\r
+\r
     }\r
     catch (Exception ex)\r
     {\r
@@ -2769,7 +2802,7 @@ public void drop(DropTargetDropEvent evt)
 \r
           FastaFile ff = new FastaFile();\r
           Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
-          c.setContents(new StringSelection(ff.print(sequences)), this);\r
+          c.setContents(new StringSelection(ff.print(sequences)), Desktop.instance);\r
 \r
           this.paste(false);\r
         }\r