From ef6291f17491f1c426e2cad44021c31f609e2808 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 21 Jul 2006 08:46:41 +0000
Subject: [PATCH] Show hide cols and rows

---
 src/jalview/gui/AlignFrame.java |   63 ++++++++++++++++++++++++++++++++++-----
 1 file changed, 56 insertions(+), 7 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d6143bf..325a676 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -352,8 +352,14 @@ public class AlignFrame
 
       if (viewport.hasHiddenColumns)
       {
-     //  System.out.println("PROMPT USER HERE");
-     //   omitHidden = viewport.getSelectionAsString();
+        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+            "The Alignment contains hidden columns."
+            + "\nDo you want to save only the visible alignment?",
+            "Save / Omit Hidden Columns",
+            JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+        if (reply == JOptionPane.YES_OPTION)
+          omitHidden = viewport.getSelectionAsString();
       }
 
       String output = new FormatAdapter().formatSequences(
@@ -404,8 +410,14 @@ public class AlignFrame
 
     if(viewport.hasHiddenColumns)
     {
-   //   System.out.println("PROMPT USER HERE");
-   //   omitHidden = viewport.getSelectionAsString();
+      int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+          "The Alignment contains hidden columns."
+      +"\nDo you want to output only the visible alignment?",
+      "Save / Omit Hidden Columns",
+      JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+      if(reply==JOptionPane.YES_OPTION)
+       omitHidden = viewport.getSelectionAsString();
     }
 
     cap.setText(new FormatAdapter().formatSequences(
@@ -837,9 +849,7 @@ public class AlignFrame
            for(int i=0; i<hc.size(); i++)
            {
              int [] region = (int[]) hc.elementAt(i);
-             for(int j=region[0]; j<region[1]+1; j++)
-               af.viewport.getColumnSelection().addElement(j);
-             af.viewport.getColumnSelection().hideColumns(region[0], af.viewport);
+             af.viewport.hideColumns(region[0], region[1]);
            }
          }
 
@@ -1389,6 +1399,45 @@ public class AlignFrame
     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
   }
 
+  public void showAllSeqs_actionPerformed(ActionEvent e)
+  {
+    viewport.showAllHiddenSeqs();
+    repaint();
+  }
+
+  public void showAllColumns_actionPerformed(ActionEvent e)
+  {
+    viewport.getColumnSelection().revealAllHiddenColumns(viewport);
+  }
+
+  public void hideSelSequences_actionPerformed(ActionEvent e)
+  {
+    if(viewport.getSelectionGroup()==null)
+      return;
+
+    SequenceI [] seqs = viewport.getSelectionGroup().getSequencesInOrder(
+        viewport.alignment
+          );
+
+    for(int i=0; i<seqs.length; i++)
+    {
+      viewport.hideSequence(seqs[i]);
+    }
+    repaint();
+  }
+
+  public void hideSelColumns_actionPerformed(ActionEvent e)
+  {
+    viewport.hideSelectedColumns();
+    repaint();
+  }
+
+  public void hiddenMarkers_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
+    repaint();
+  }
+
   /**
    * DOCUMENT ME!
    *
-- 
1.7.10.2