File Parsing returns Alignments, not Sequence[]

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

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 1cd1c6a..4773c26 100755 (executable)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -170,12 +170,12 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     public void ok_actionPerformed(ActionEvent e)\r
     {\r
         String format = new IdentifyFile().Identify(getText(), "Paste");\r
-        SequenceI[] sequences = null;\r
+        Alignment al = null;\r
 \r
         if (FormatAdapter.isValidFormat(format))\r
         {\r
           try{\r
-            sequences = new FormatAdapter().readFile(getText(), "Paste", format);\r
+            al = new FormatAdapter().readFile(getText(), "Paste", format);\r
           }catch(java.io.IOException ex)\r
           {\r
             JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
@@ -185,18 +185,18 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
           }\r
         }\r
 \r
-        if (sequences != null)\r
+        if (al != null)\r
         {\r
           if(viewport!=null)\r
           {\r
-            for(int i=0; i<sequences.length; i++)\r
-              viewport.getAlignment().addSequence(sequences[i]);\r
+            for(int i=0; i<al.getHeight(); i++)\r
+              viewport.getAlignment().addSequence(al.getSequenceAt(i));\r
 \r
             viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
           }\r
           else\r
           {\r
-            AlignFrame af = new AlignFrame(new Alignment(sequences),\r
+            AlignFrame af = new AlignFrame(al,\r
                                            AlignFrame.DEFAULT_WIDTH,\r
                                            AlignFrame.DEFAULT_HEIGHT);\r
             af.currentFileFormat = format;\r