JAL-2154 ENA specific Ensembl canonical db prefixes

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

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 74c58b7..7ef2a68 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -290,11 +290,12 @@ public class ColumnSelection
   /**
    * Returns a list of selected columns. The list contains no duplicates but is
    * not necessarily ordered. It also may include columns hidden from the
-   * current view
+   * current view. This returns a copy of the actual list, and changes to the
+   * copy will not affect the selection.
    */
   public List<Integer> getSelected()
   {
-    return selection.getList();
+    return new ArrayList<Integer>(selection.getList());
   }
 
   /**
@@ -985,7 +986,7 @@ public class ColumnSelection
           SequenceI[] seqs)
   {
     int i, iSize = seqs.length;
-    String selection[] = new String[iSize];
+    String selections[] = new String[iSize];
     if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
       for (i = 0; i < iSize; i++)
@@ -1027,18 +1028,18 @@ public class ColumnSelection
           visibleSeq.append(seqs[i].getSequence(blockStart, end));
         }
 
-        selection[i] = visibleSeq.toString();
+        selections[i] = visibleSeq.toString();
       }
     }
     else
     {
       for (i = 0; i < iSize; i++)
       {
-        selection[i] = seqs[i].getSequenceAsString(start, end);
+        selections[i] = seqs[i].getSequenceAsString(start, end);
       }
     }
 
-    return selection;
+    return selections;
   }
 
   /**
@@ -1651,14 +1652,130 @@ public class ColumnSelection
     return hashCode;
   }
 
+  /**
+   * Answers true if comparing to a ColumnSelection with the same selected
+   * columns and hidden columns, else false
+   */
   @Override
   public boolean equals(Object obj)
   {
-    if (obj instanceof ColumnSelection)
+    if (!(obj instanceof ColumnSelection))
     {
-      return hashCode() == obj.hashCode();
+      return false;
     }
-    return false;
+    ColumnSelection that = (ColumnSelection) obj;
+
+    /*
+     * check columns selected are either both null, or match
+     */
+    if (this.selection == null)
+    {
+      if (that.selection != null)
+      {
+        return false;
+      }
+    }
+    if (!this.selection.equals(that.selection))
+    {
+      return false;
+    }
+
+    /*
+     * check hidden columns are either both null, or match
+     */
+    if (this.hiddenColumns == null)
+    {
+      return (that.hiddenColumns == null);
+    }
+    if (that.hiddenColumns == null
+            || that.hiddenColumns.size() != this.hiddenColumns.size())
+    {
+      return false;
+    }
+    int i = 0;
+    for (int[] thisRange : hiddenColumns)
+    {
+      int[] thatRange = that.hiddenColumns.get(i++);
+      if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
+      {
+        return false;
+      }
+    }
+    return true;
+  }
+
+  /**
+   * Updates the column selection depending on the parameters, and returns true
+   * if any change was made to the selection
+   * 
+   * @param markedColumns
+   *          a set identifying marked columns (base 0)
+   * @param startCol
+   *          the first column of the range to operate over (base 0)
+   * @param endCol
+   *          the last column of the range to operate over (base 0)
+   * @param invert
+   *          if true, deselect marked columns and select unmarked
+   * @param extendCurrent
+   *          if true, extend rather than replacing the current column selection
+   * @param toggle
+   *          if true, toggle the selection state of marked columns
+   * 
+   * @return
+   */
+  public boolean markColumns(BitSet markedColumns, int startCol,
+          int endCol, boolean invert, boolean extendCurrent, boolean toggle)
+  {
+    boolean changed = false;
+    if (!extendCurrent && !toggle)
+    {
+      changed = !this.isEmpty();
+      clear();
+    }
+    if (invert)
+    {
+      // invert only in the currently selected sequence region
+      int i = markedColumns.nextClearBit(startCol);
+      int ibs = markedColumns.nextSetBit(startCol);
+      while (i >= startCol && i <= endCol)
+      {
+        if (ibs < 0 || i < ibs)
+        {
+          changed = true;
+          if (toggle && contains(i))
+          {
+            removeElement(i++);
+          }
+          else
+          {
+            addElement(i++);
+          }
+        }
+        else
+        {
+          i = markedColumns.nextClearBit(ibs);
+          ibs = markedColumns.nextSetBit(i);
+        }
+      }
+    }
+    else
+    {
+      int i = markedColumns.nextSetBit(startCol);
+      while (i >= startCol && i <= endCol)
+      {
+        changed = true;
+        if (toggle && contains(i))
+        {
+          removeElement(i);
+        }
+        else
+        {
+          addElement(i);
+        }
+        i = markedColumns.nextSetBit(i + 1);
+      }
+    }
+    return changed;
   }
 
 }