From 54adeabf66bf1b5f2ef56855d3ba940602a854eb Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 23 Jan 2015 14:10:20 +0000
Subject: [PATCH] JAL-969 drop the hiddenColumns flag in favour of checking
 current state of columnSelection

---
 src/jalview/gui/AlignViewport.java           |   31 ++---------------------
 src/jalview/viewmodel/AlignmentViewport.java |   35 +++++++++++---------------
 2 files changed, 17 insertions(+), 49 deletions(-)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 4df9a62..a2ed7cd 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -195,16 +195,7 @@ public class AlignViewport extends AlignmentViewport implements
     setAlignment(al);
     if (hiddenColumns != null)
     {
-      this.colSel = hiddenColumns;
-      if (hiddenColumns.getHiddenColumns() != null
-              && hiddenColumns.getHiddenColumns().size() > 0)
-      {
-        hasHiddenColumns = true;
-      }
-      else
-      {
-        hasHiddenColumns = false;
-      }
+      colSel = hiddenColumns;
     }
     init();
   }
@@ -251,16 +242,7 @@ public class AlignViewport extends AlignmentViewport implements
     setAlignment(al);
     if (hiddenColumns != null)
     {
-      this.colSel = hiddenColumns;
-      if (hiddenColumns.getHiddenColumns() != null
-              && hiddenColumns.getHiddenColumns().size() > 0)
-      {
-        hasHiddenColumns = true;
-      }
-      else
-      {
-        hasHiddenColumns = false;
-      }
+      colSel = hiddenColumns;
     }
     init();
   }
@@ -1019,15 +1001,6 @@ public class AlignViewport extends AlignmentViewport implements
   }
 
   /**
-   * 
-   * @return true if view has hidden columns
-   */
-  public boolean hasHiddenColumns()
-  {
-    return hasHiddenColumns;
-  }
-
-  /**
    * when set, view will scroll to show the highlighted position
    */
   public boolean followHighlight = true;
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index a48c910..9cd9bfd 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -637,10 +637,6 @@ public abstract class AlignmentViewport implements AlignViewportI
   public void setHiddenColumns(ColumnSelection colsel)
   {
     this.colSel = colsel;
-    if (colSel.getHiddenColumns() != null)
-    {
-      hasHiddenColumns = true;
-    }
   }
 
   @Override
@@ -676,11 +672,17 @@ public abstract class AlignmentViewport implements AlignViewportI
     this.hiddenRepSequences = hiddenRepSequences;
   }
 
-  protected boolean hasHiddenColumns = false;
+  @Override
+  public boolean hasHiddenColumns()
+  {
+    return colSel != null && colSel.hasHiddenColumns();
+  }
 
   public void updateHiddenColumns()
   {
-    hasHiddenColumns = colSel.hasHiddenColumns();
+    // this method doesn't really do anything now. But - it could, since a
+    // column Selection could be in the process of modification
+    // hasHiddenColumns = colSel.hasHiddenColumns();
   }
 
   protected boolean hasHiddenRows = false;
@@ -864,7 +866,6 @@ public abstract class AlignmentViewport implements AlignViewportI
     colSel.hideSelectedColumns();
     setSelectionGroup(null);
 
-    hasHiddenColumns = true;
   }
 
   public void hideColumns(int start, int end)
@@ -877,23 +878,17 @@ public abstract class AlignmentViewport implements AlignViewportI
     {
       colSel.hideColumns(start, end);
     }
-
-    hasHiddenColumns = true;
   }
 
   public void showColumn(int col)
   {
     colSel.revealHiddenColumns(col);
-    if (colSel.getHiddenColumns() == null)
-    {
-      hasHiddenColumns = false;
-    }
+
   }
 
   public void showAllHiddenColumns()
   {
     colSel.revealAllHiddenColumns();
-    hasHiddenColumns = false;
   }
 
   // common hide/show seq stuff
@@ -1113,8 +1108,7 @@ public abstract class AlignmentViewport implements AlignViewportI
   public jalview.datamodel.CigarArray getViewAsCigars(
           boolean selectedRegionOnly)
   {
-    return new jalview.datamodel.CigarArray(alignment,
-            (hasHiddenColumns ? colSel : null),
+    return new jalview.datamodel.CigarArray(alignment, colSel,
             (selectedRegionOnly ? selectionGroup : null));
   }
 
@@ -1132,7 +1126,8 @@ public abstract class AlignmentViewport implements AlignViewportI
           boolean selectedOnly, boolean markGroups)
   {
     return new AlignmentView(alignment, colSel, selectionGroup,
-            hasHiddenColumns, selectedOnly, markGroups);
+            colSel != null && colSel.hasHiddenColumns(), selectedOnly,
+            markGroups);
   }
 
 
@@ -1158,7 +1153,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     }
 
     selection = new String[iSize];
-    if (hasHiddenColumns)
+    if (colSel != null && colSel.hasHiddenColumns())
     {
       selection = colSel.getVisibleSequenceStrings(start, end, seqs);
     }
@@ -1183,7 +1178,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
     do
     {
-      if (hasHiddenColumns)
+      if (colSel != null && colSel.hasHiddenColumns())
       {
         if (start == 0)
         {
@@ -1204,7 +1199,7 @@ public abstract class AlignmentViewport implements AlignViewportI
       regions.addElement(new int[]
       { start, end });
 
-      if (hasHiddenColumns)
+      if (colSel != null && colSel.hasHiddenColumns())
       {
         start = colSel.adjustForHiddenColumns(end);
         start = colSel.getHiddenBoundaryLeft(start) + 1;
-- 
1.7.10.2