getViewAsString can ignore sequenceGroup

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 325a676..2ce8f06 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -359,16 +359,13 @@ public class AlignFrame
             JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);\r
 \r
         if (reply == JOptionPane.YES_OPTION)\r
-          omitHidden = viewport.getSelectionAsString();\r
+          omitHidden = viewport.getViewAsString(false);\r
       }\r
 \r
       String output = new FormatAdapter().formatSequences(\r
           format,\r
           viewport.alignment.getSequencesArray(),\r
-          null);\r
-          //viewport.getSelectionAsNewSequence(),\r
-          //omitHidden) ;\r
-\r
+          omitHidden);\r
 \r
       if (output == null)\r
       {\r
@@ -400,12 +397,6 @@ public class AlignFrame
    */\r
   protected void outputText_actionPerformed(ActionEvent e)\r
   {\r
-    CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
-    Desktop.addInternalFrame(cap,\r
-                             "Alignment output - " + e.getActionCommand(), 600,\r
-                             500);\r
-\r
-\r
     String [] omitHidden = null;\r
 \r
     if(viewport.hasHiddenColumns)\r
@@ -417,12 +408,20 @@ public class AlignFrame
       JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);\r
 \r
       if(reply==JOptionPane.YES_OPTION)\r
-       omitHidden = viewport.getSelectionAsString();\r
+      {\r
+        omitHidden = viewport.getViewAsString(false);\r
+      }\r
     }\r
 \r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+    Desktop.addInternalFrame(cap,\r
+                             "Alignment output - " + e.getActionCommand(), 600,\r
+                             500);\r
+\r
+\r
     cap.setText(new FormatAdapter().formatSequences(\r
         e.getActionCommand(),\r
-        viewport.getSelectionAsNewSequence(),\r
+        viewport.alignment.getSequencesArray(),\r
         omitHidden));\r
   }\r
 \r
@@ -690,7 +689,7 @@ public class AlignFrame
 \r
     if (viewport.hasHiddenColumns)\r
     {\r
-      omitHidden = viewport.getSelectionAsString();\r
+      omitHidden = viewport.getViewAsString(true);\r
     }\r
 \r
     String output = new FormatAdapter().formatSequences(\r
@@ -849,7 +848,7 @@ public class AlignFrame
            for(int i=0; i<hc.size(); i++)\r
            {\r
              int [] region = (int[]) hc.elementAt(i);\r
-             af.viewport.hideColumns(region[0], region[1]);\r
+             af.viewport.hideColumns(region[0], region[1]+1);\r
            }\r
          }\r
 \r
@@ -2614,11 +2613,10 @@ public class AlignFrame
 \r
 \r
 \r
-\r
 public void showTranslation_actionPerformed(ActionEvent e)\r
 {\r
   SequenceI [] selection = viewport.getSelectionAsNewSequence();\r
-  String [] seqstring = viewport.getSelectionAsString();\r
+  String [] seqstring = viewport.getViewAsString(true);\r
 \r
   int s, sSize = selection.length;\r
   SequenceI [] newSeq = new SequenceI[sSize];\r