c&p changed

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 2753652..0548646 100755 (executable)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -276,7 +276,7 @@ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
 \r
  public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
  {\r
-   CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
+   CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
    int accept =  JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",\r
                                        JOptionPane.YES_NO_CANCEL_OPTION,\r
                                        JOptionPane.PLAIN_MESSAGE,\r

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 8294469..d85fabc 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -525,9 +525,8 @@ public class PopupMenu extends JPopupMenu
 \r
   protected void analyze_actionPerformed(ActionEvent e)\r
   {\r
-     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
+     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
      JInternalFrame frame = new JInternalFrame();\r
-     cap.formatForOutput();\r
      frame.setContentPane(cap);\r
      Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
      SequenceGroup sg = getGroup();\r

diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index 7770ced..afe7b6e 100755 (executable)
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -13,7 +13,7 @@ public class SequenceFeatureFetcher implements Runnable
   AlignmentPanel ap;\r
   ArrayList unknownSequences;\r
   JInternalFrame outputFrame = new JInternalFrame();\r
-  CutAndPasteTransfer output = new CutAndPasteTransfer(false);\r
+  CutAndPasteTransfer output = new CutAndPasteTransfer();\r
   StringBuffer sbuffer = new StringBuffer();\r
 \r
   public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)\r
@@ -103,7 +103,6 @@ public class SequenceFeatureFetcher implements Runnable
   findMissingIds(align);\r
   if(sbuffer.length()>0)\r
   {\r
-    output.formatForOutput();\r
     outputFrame.setContentPane(output);\r
     output.setText("Your sequences have been matched to Uniprot. Some of the ids have been\n"\r
                    +"altered, most likely the start/end residue will have been updated.\n"\r

diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index ace3e0d..160d9f0 100755 (executable)
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -12,13 +12,11 @@ import java.awt.*;
 public class WSWUBlastClient\r
 {\r
   JInternalFrame outputFrame = new JInternalFrame();\r
-  CutAndPasteTransfer output = new CutAndPasteTransfer(false);\r
+  CutAndPasteTransfer output = new CutAndPasteTransfer();\r
   int jobsRunning = 0;\r
 \r
   public WSWUBlastClient(AlignmentI al, ArrayList ids)\r
   {\r
-\r
-    output.formatForOutput();\r
     outputFrame.setContentPane(output);\r
     output.setText("To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."\r
                 +"\nIn order to display these features, try changing the names of your sequences to the ids suggested below.");\r