JAL-2446 merged to spike branch

[jalview.git] / src / jalview / datamodel / AlignmentView.java

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 6698d49..9ca70f2 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -141,13 +141,14 @@ public class AlignmentView
    *          the view
    */
   public AlignmentView(AlignmentI alignment,
-          ColumnSelection columnSelection, SequenceGroup selection,
+ HiddenColumns hidden,
+          SequenceGroup selection,
           boolean hasHiddenColumns, boolean selectedRegionOnly,
           boolean recordGroups)
   {
     // refactored from AlignViewport.getAlignmentView(selectedOnly);
     this(new jalview.datamodel.CigarArray(alignment,
-            (hasHiddenColumns ? columnSelection : null),
+            (hasHiddenColumns ? hidden : null),
             (selectedRegionOnly ? selection : null)),
             (selectedRegionOnly && selection != null) ? selection
                     .getStartRes() : 0);
@@ -330,13 +331,13 @@ public class AlignmentView
    *          char
    * @return Object[] { SequenceI[], ColumnSelection}
    */
-  public Object[] getAlignmentAndColumnSelection(char gapCharacter)
+  public Object[] getAlignmentAndHiddenColumns(char gapCharacter)
   {
-    ColumnSelection colsel = new ColumnSelection();
+    HiddenColumns hidden = new HiddenColumns();
 
     return new Object[] {
-        SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
-                contigs), colsel };
+        SeqCigar.createAlignmentSequences(sequences, gapCharacter, hidden,
+                contigs), hidden };
   }
 
   /**
@@ -710,7 +711,8 @@ public class AlignmentView
     if (contigs != null && contigs.length > 0)
     {
       SequenceI[] alignment = new SequenceI[sequences.length];
-      ColumnSelection columnselection = new ColumnSelection();
+      // ColumnSelection columnselection = new ColumnSelection();
+      HiddenColumns hidden = new HiddenColumns();
       if (contigs != null && contigs.length > 0)
       {
         int start = 0;
@@ -823,7 +825,7 @@ public class AlignmentView
             }
           }
           // mark hidden segment as hidden in the new alignment
-          columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2]
+          hidden.hideColumns(nwidth, nwidth + contigs[contig + 2]
                   - 1);
           nwidth += contigs[contig + 2];
         }
@@ -901,7 +903,7 @@ public class AlignmentView
           }
         }
       }
-      return new Object[] { alignment, columnselection };
+      return new Object[] { alignment, hidden };
     }
     else
     {
@@ -916,11 +918,11 @@ public class AlignmentView
       }
       if (nvismsa[0] != null)
       {
-        return new Object[] { nvismsa[0], new ColumnSelection() };
+        return new Object[] { nvismsa[0], new HiddenColumns() };
       }
       else
       {
-        return getAlignmentAndColumnSelection(gapCharacter);
+        return getAlignmentAndHiddenColumns(gapCharacter);
       }
     }
   }
@@ -970,14 +972,14 @@ public class AlignmentView
       if (start < fwidth)
       {
         viscontigs[nvis] = start;
-        viscontigs[nvis + 1] = fwidth; // end is inclusive
+        viscontigs[nvis + 1] = fwidth - 1; // end is inclusive
         nvis += 2;
       }
       return viscontigs;
     }
     else
     {
-      return new int[] { 0, width };
+      return new int[] { 0, width - 1 };
     }
   }
 
@@ -1135,7 +1137,7 @@ public class AlignmentView
   }
 
   public static void testSelectionViews(AlignmentI alignment,
-          ColumnSelection csel, SequenceGroup selection)
+          HiddenColumns hidden, SequenceGroup selection)
   {
     System.out.println("Testing standard view creation:\n");
     AlignmentView view = null;
@@ -1143,7 +1145,7 @@ public class AlignmentView
     {
       System.out
               .println("View with no hidden columns, no limit to selection, no groups to be collected:");
-      view = new AlignmentView(alignment, csel, selection, false, false,
+      view = new AlignmentView(alignment, hidden, selection, false, false,
               false);
       summariseAlignmentView(view, System.out);
 
@@ -1157,7 +1159,7 @@ public class AlignmentView
     {
       System.out
               .println("View with no hidden columns, no limit to selection, and all groups to be collected:");
-      view = new AlignmentView(alignment, csel, selection, false, false,
+      view = new AlignmentView(alignment, hidden, selection, false, false,
               true);
       summariseAlignmentView(view, System.out);
     } catch (Exception e)
@@ -1170,7 +1172,7 @@ public class AlignmentView
     {
       System.out
               .println("View with no hidden columns, limited to selection and no groups to be collected:");
-      view = new AlignmentView(alignment, csel, selection, false, true,
+      view = new AlignmentView(alignment, hidden, selection, false, true,
               false);
       summariseAlignmentView(view, System.out);
     } catch (Exception e)
@@ -1183,7 +1185,7 @@ public class AlignmentView
     {
       System.out
               .println("View with no hidden columns, limited to selection, and all groups to be collected:");
-      view = new AlignmentView(alignment, csel, selection, false, true,
+      view = new AlignmentView(alignment, hidden, selection, false, true,
               true);
       summariseAlignmentView(view, System.out);
     } catch (Exception e)
@@ -1196,7 +1198,7 @@ public class AlignmentView
     {
       System.out
               .println("View *with* hidden columns, no limit to selection, no groups to be collected:");
-      view = new AlignmentView(alignment, csel, selection, true, false,
+      view = new AlignmentView(alignment, hidden, selection, true, false,
               false);
       summariseAlignmentView(view, System.out);
     } catch (Exception e)
@@ -1209,7 +1211,7 @@ public class AlignmentView
     {
       System.out
               .println("View *with* hidden columns, no limit to selection, and all groups to be collected:");
-      view = new AlignmentView(alignment, csel, selection, true, false,
+      view = new AlignmentView(alignment, hidden, selection, true, false,
               true);
       summariseAlignmentView(view, System.out);
     } catch (Exception e)
@@ -1222,7 +1224,7 @@ public class AlignmentView
     {
       System.out
               .println("View *with* hidden columns, limited to selection and no groups to be collected:");
-      view = new AlignmentView(alignment, csel, selection, true, true,
+      view = new AlignmentView(alignment, hidden, selection, true, true,
               false);
       summariseAlignmentView(view, System.out);
     } catch (Exception e)
@@ -1235,7 +1237,8 @@ public class AlignmentView
     {
       System.out
               .println("View *with* hidden columns, limited to selection, and all groups to be collected:");
-      view = new AlignmentView(alignment, csel, selection, true, true, true);
+      view = new AlignmentView(alignment, hidden, selection, true, true,
+              true);
       summariseAlignmentView(view, System.out);
     } catch (Exception e)
     {