From 048a384fa19ac37fbe2b63bbba139d5fa17107c5 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 27 Jun 2016 14:03:09 +0100
Subject: [PATCH] JAL-2133 refactored duplicated code to AlignmentViewport

---
 src/jalview/appletgui/APopupMenu.java        |   33 ++++----------------------
 src/jalview/gui/PopupMenu.java               |   23 +-----------------
 src/jalview/viewmodel/AlignmentViewport.java |   33 ++++++++++++++++++++++++++
 3 files changed, 38 insertions(+), 51 deletions(-)

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 748954a..948c8e5 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -537,6 +537,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     MenuItem item = new MenuItem(label);
     item.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         ap.alignFrame.showURL(url, target);
@@ -545,6 +546,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     linkMenu.add(item);
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == abovePIDColour)
@@ -569,6 +571,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     }
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     Object source = evt.getSource();
@@ -1299,35 +1302,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   void hideSequences(boolean representGroup)
   {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg == null || sg.getSize() < 1)
-    {
-      ap.av.hideSequence(new SequenceI[] { seq });
-      return;
-    }
-
-    ap.av.setSelectionGroup(null);
-
-    if (representGroup)
-    {
-      ap.av.hideRepSequences(seq, sg);
-
-      return;
-    }
-
-    int gsize = sg.getSize();
-    SequenceI[] hseqs;
-
-    hseqs = new SequenceI[gsize];
-
-    int index = 0;
-    for (int i = 0; i < gsize; i++)
-    {
-      hseqs[index++] = sg.getSequenceAt(i);
-    }
-
-    ap.av.hideSequence(hseqs);
-    ap.av.sendSelection();
+    ap.av.hideSequences(seq, representGroup);
   }
 
   /**
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index e64d43f..497f3ba 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -2270,28 +2270,7 @@ public class PopupMenu extends JPopupMenu
 
   void hideSequences(boolean representGroup)
   {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg == null || sg.getSize() < 1)
-    {
-      ap.av.hideSequence(new SequenceI[] { sequence });
-      return;
-    }
-
-    ap.av.setSelectionGroup(null);
-
-    if (representGroup)
-    {
-      ap.av.hideRepSequences(sequence, sg);
-
-      return;
-    }
-
-    int gsize = sg.getSize();
-    SequenceI[] hseqs = sg.getSequences().toArray(new SequenceI[gsize]);
-
-    ap.av.hideSequence(hseqs);
-    // refresh(); TODO: ? needed ?
-    ap.av.sendSelection();
+    ap.av.hideSequences(sequence, representGroup);
   }
 
   public void copy_actionPerformed()
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 91ee3c1..eab4aa5 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1413,6 +1413,39 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   /**
+   * Hides the specified sequence, or the sequences it represents
+   * 
+   * @param sequence
+   *          the sequence to hide, or keep as representative
+   * @param representGroup
+   *          if true, hide the current selection group except for the
+   *          representative sequence
+   */
+  public void hideSequences(SequenceI sequence, boolean representGroup)
+  {
+    if (selectionGroup == null || selectionGroup.getSize() < 1)
+    {
+      hideSequence(new SequenceI[] { sequence });
+      return;
+    }
+
+    if (representGroup)
+    {
+      hideRepSequences(sequence, selectionGroup);
+      setSelectionGroup(null);
+      return;
+    }
+
+    int gsize = selectionGroup.getSize();
+    SequenceI[] hseqs = selectionGroup.getSequences().toArray(
+            new SequenceI[gsize]);
+
+    hideSequence(hseqs);
+    setSelectionGroup(null);
+    sendSelection();
+  }
+
+  /**
    * Set visibility for any annotations for the given sequence.
    * 
    * @param sequenceI
-- 
1.7.10.2