Show hide cols and rows

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d6143bf..325a676 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -352,8 +352,14 @@ public class AlignFrame
 \r
       if (viewport.hasHiddenColumns)\r
       {\r
-     //  System.out.println("PROMPT USER HERE");\r
-     //   omitHidden = viewport.getSelectionAsString();\r
+        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+            "The Alignment contains hidden columns."\r
+            + "\nDo you want to save only the visible alignment?",\r
+            "Save / Omit Hidden Columns",\r
+            JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);\r
+\r
+        if (reply == JOptionPane.YES_OPTION)\r
+          omitHidden = viewport.getSelectionAsString();\r
       }\r
 \r
       String output = new FormatAdapter().formatSequences(\r
@@ -404,8 +410,14 @@ public class AlignFrame
 \r
     if(viewport.hasHiddenColumns)\r
     {\r
-   //   System.out.println("PROMPT USER HERE");\r
-   //   omitHidden = viewport.getSelectionAsString();\r
+      int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+          "The Alignment contains hidden columns."\r
+      +"\nDo you want to output only the visible alignment?",\r
+      "Save / Omit Hidden Columns",\r
+      JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);\r
+\r
+      if(reply==JOptionPane.YES_OPTION)\r
+       omitHidden = viewport.getSelectionAsString();\r
     }\r
 \r
     cap.setText(new FormatAdapter().formatSequences(\r
@@ -837,9 +849,7 @@ public class AlignFrame
            for(int i=0; i<hc.size(); i++)\r
            {\r
              int [] region = (int[]) hc.elementAt(i);\r
-             for(int j=region[0]; j<region[1]+1; j++)\r
-               af.viewport.getColumnSelection().addElement(j);\r
-             af.viewport.getColumnSelection().hideColumns(region[0], af.viewport);\r
+             af.viewport.hideColumns(region[0], region[1]);\r
            }\r
          }\r
 \r
@@ -1389,6 +1399,45 @@ public class AlignFrame
     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());\r
   }\r
 \r
+  public void showAllSeqs_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.showAllHiddenSeqs();\r
+    repaint();\r
+  }\r
+\r
+  public void showAllColumns_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.getColumnSelection().revealAllHiddenColumns(viewport);\r
+  }\r
+\r
+  public void hideSelSequences_actionPerformed(ActionEvent e)\r
+  {\r
+    if(viewport.getSelectionGroup()==null)\r
+      return;\r
+\r
+    SequenceI [] seqs = viewport.getSelectionGroup().getSequencesInOrder(\r
+        viewport.alignment\r
+          );\r
+\r
+    for(int i=0; i<seqs.length; i++)\r
+    {\r
+      viewport.hideSequence(seqs[i]);\r
+    }\r
+    repaint();\r
+  }\r
+\r
+  public void hideSelColumns_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.hideSelectedColumns();\r
+    repaint();\r
+  }\r
+\r
+  public void hiddenMarkers_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());\r
+    repaint();\r
+  }\r
+\r
   /**\r
    * DOCUMENT ME!\r
    *\r