X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=7ef2a68d3a2aa8c1d0a59f0524b08b4a00291094;hb=a22250ded2ef2b4a65e342066762008b4f380bbd;hp=cfe4685f5c335c18cbd96f18948c8015256b8629;hpb=2e5d563a1a639e338a9b2e9742ebd4a96c6c3e45;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index cfe4685..7ef2a68 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -20,6 +20,7 @@
  */
 package jalview.datamodel;
 
+import jalview.util.Comparison;
 import jalview.util.ShiftList;
 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
@@ -31,10 +32,14 @@ import java.util.List;
 import java.util.Vector;
 
 /**
- * NOTE: Columns are zero based.
+ * Data class holding the selected columns and hidden column ranges for a view.
+ * Ranges are base 1.
  */
 public class ColumnSelection
 {
+  /**
+   * A class to hold an efficient representation of selected columns
+   */
   private class IntList
   {
     /*
@@ -184,9 +189,47 @@ public class ColumnSelection
     {
       return selected.get(0) ? 0 : selected.nextSetBit(0);
     }
+
+    /**
+     * @return a series of selection intervals along the range
+     */
+    public List<int[]> getRanges()
+    {
+      List<int[]> rlist = new ArrayList<int[]>();
+      if (selected.isEmpty())
+      {
+        return rlist;
+      }
+      int next = selected.nextSetBit(0), clear = -1;
+      while (next != -1)
+      {
+        clear = selected.nextClearBit(next);
+        rlist.add(new int[] { next, clear - 1 });
+        next = selected.nextSetBit(clear);
+      }
+      return rlist;
+    }
+
+    @Override
+    public int hashCode()
+    {
+      // TODO Auto-generated method stub
+      return selected.hashCode();
+    }
+
+    @Override
+    public boolean equals(Object obj)
+    {
+      if (obj instanceof IntList)
+      {
+        return ((IntList) obj).selected.equals(selected);
+      }
+      return false;
+    }
   }
 
-  IntList selected = new IntList();
+  IntList selection = new IntList();
+
   /*
    * list of hidden column [start, end] ranges; the list is maintained in
    * ascending start column order
@@ -201,7 +244,7 @@ public class ColumnSelection
    */
   public void addElement(int col)
   {
-    selected.add(col);
+    selection.add(col);
   }
 
   /**
@@ -209,7 +252,7 @@ public class ColumnSelection
    */
   public void clear()
   {
-    selected.clear();
+    selection.clear();
   }
 
   /**
@@ -220,7 +263,7 @@ public class ColumnSelection
    */
   public void removeElement(int col)
   {
-    selected.remove(col);
+    selection.remove(col);
   }
 
   /**
@@ -237,9 +280,9 @@ public class ColumnSelection
     for (int i = start; i < end; i++)
     {
       colInt = new Integer(i);
-      if (selected.contains(colInt))
+      if (selection.contains(colInt))
       {
-        selected.remove(colInt);
+        selection.remove(colInt);
       }
     }
   }
@@ -247,11 +290,21 @@ 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 selected.getList();
+    return new ArrayList<Integer>(selection.getList());
+  }
+
+  /**
+   * @return list of int arrays containing start and end column position for
+   *         runs of selected columns ordered from right to left.
+   */
+  public List<int[]> getSelectedRanges()
+  {
+    return selection.getRanges();
   }
 
   /**
@@ -259,11 +312,11 @@ public class ColumnSelection
    * @param col
    *          index to search for in column selection
    * 
-   * @return true if Integer(col) is in selection.
+   * @return true if col is selected
    */
   public boolean contains(int col)
   {
-    return selected.isSelected(col);
+    return (col > -1) ? selection.isSelected(col) : false;
   }
 
   /**
@@ -271,7 +324,7 @@ public class ColumnSelection
    */
   public boolean isEmpty()
   {
-    return selected == null || selected.isEmpty();
+    return selection == null || selection.isEmpty();
   }
 
   /**
@@ -281,11 +334,11 @@ public class ColumnSelection
    */
   public int getMax()
   {
-    if (selected.isEmpty())
+    if (selection.isEmpty())
     {
       return -1;
     }
-    return selected.getMaxColumn();
+    return selection.getMaxColumn();
   }
 
   /**
@@ -295,11 +348,11 @@ public class ColumnSelection
    */
   public int getMin()
   {
-    if (selected.isEmpty())
+    if (selection.isEmpty())
     {
       return 1000000000;
     }
-    return selected.getMinColumn();
+    return selection.getMinColumn();
   }
 
   /**
@@ -313,7 +366,7 @@ public class ColumnSelection
   public List<int[]> compensateForEdit(int start, int change)
   {
     List<int[]> deletedHiddenColumns = null;
-    selected.compensateForEdits(start, change);
+    selection.compensateForEdits(start, change);
 
     if (hiddenColumns != null)
     {
@@ -363,7 +416,7 @@ public class ColumnSelection
   private void compensateForDelEdits(int start, int change)
   {
 
-    selected.compensateForEdits(start, change);
+    selection.compensateForEdits(start, change);
 
     if (hiddenColumns != null)
     {
@@ -540,12 +593,12 @@ public class ColumnSelection
             hiddenColumns = null;
           }
         }
-        if (selected != null && selected.size() > 0)
+        if (selection != null && selection.size() > 0)
         {
-          selected.pruneColumnList(shifts);
-          if (selected != null && selected.size() == 0)
+          selection.pruneColumnList(shifts);
+          if (selection != null && selection.size() == 0)
           {
-            selected = null;
+            selection = null;
           }
         }
         // and shift the rest.
@@ -569,7 +622,7 @@ public class ColumnSelection
    * Return absolute column index for a visible column index
    * 
    * @param column
-   *          int column index in alignment view
+   *          int column index in alignment view (count from zero)
    * @return alignment column index for column
    */
   public int adjustForHiddenColumns(int column)
@@ -623,6 +676,10 @@ public class ColumnSelection
 
   /**
    * Use this method to determine where the next hiddenRegion starts
+   * 
+   * @param hiddenRegion
+   *          index of hidden region (counts from 0)
+   * @return column number in visible view
    */
   public int findHiddenRegionPosition(int hiddenRegion)
   {
@@ -642,7 +699,7 @@ public class ColumnSelection
         gaps += region[1] + 1 - region[0];
         result = region[1] + 1;
         index++;
-      } while (index < hiddenRegion + 1);
+      } while (index <= hiddenRegion);
 
       result -= gaps;
     }
@@ -708,10 +765,13 @@ public class ColumnSelection
 
   public void hideSelectedColumns()
   {
-    while (!selected.isEmpty())
+    synchronized (selection)
     {
-      int column = selected.elementAt(0);
-      hideColumns(column);
+      for (int[] selregions : selection.getRanges())
+      {
+        hideColumns(selregions[0], selregions[1]);
+      }
+      selection.clear();
     }
 
   }
@@ -771,7 +831,7 @@ public class ColumnSelection
     /*
      * remaining case is that the new range follows everything else
      */
-      hiddenColumns.addElement(new int[] { start, end });
+    hiddenColumns.addElement(new int[] { start, end });
   }
 
   /**
@@ -889,12 +949,12 @@ public class ColumnSelection
   {
     if (copy != null)
     {
-      if (copy.selected != null)
+      if (copy.selection != null)
       {
-        selected = new IntList();
-        for (int i = 0, j = copy.selected.size(); i < j; i++)
+        selection = new IntList();
+        for (int i = 0, j = copy.selection.size(); i < j; i++)
         {
-          selected.add(copy.selected.elementAt(i));
+          selection.add(copy.selection.elementAt(i));
         }
       }
       if (copy.hiddenColumns != null)
@@ -926,7 +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++)
@@ -968,18 +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;
   }
 
   /**
@@ -1042,6 +1102,84 @@ public class ColumnSelection
   }
 
   /**
+   * Locate the first and last position visible for this sequence. if seq isn't
+   * visible then return the position of the left and right of the hidden
+   * boundary region, and the corresponding alignment column indices for the
+   * extent of the sequence
+   * 
+   * @param seq
+   * @return int[] { visible start, visible end, first seqpos, last seqpos,
+   *         alignment index for seq start, alignment index for seq end }
+   */
+  public int[] locateVisibleBoundsOfSequence(SequenceI seq)
+  {
+    int fpos=seq.getStart(),lpos= seq.getEnd();
+    int start = 0;
+    
+    if (hiddenColumns == null || hiddenColumns.size() == 0)
+    {
+      int ifpos = seq.findIndex(fpos) - 1, ilpos = seq.findIndex(lpos) - 1;
+      return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos };
+    }
+
+    // Simply walk along the sequence whilst watching for hidden column
+    // boundaries
+    List<int[]> regions = getHiddenColumns();
+    int spos = fpos, lastvispos = -1, rcount = 0, hideStart = seq
+            .getLength(), hideEnd = -1;
+    int visPrev = 0, visNext = 0, firstP = -1, lastP = -1;
+    boolean foundStart = false;
+    for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
+            && p < pLen; p++)
+    {
+      if (!Comparison.isGap(seq.getCharAt(p)))
+      {
+        // keep track of first/last column
+        // containing sequence data regardless of visibility
+        if (firstP == -1)
+        {
+          firstP = p;
+        }
+        lastP = p;
+        // update hidden region start/end
+        while (hideEnd < p && rcount < regions.size())
+        {
+          int[] region = regions.get(rcount++);
+          visPrev = visNext;
+          visNext += region[0] - visPrev;
+          hideStart = region[0];
+          hideEnd = region[1];
+        }
+        if (hideEnd < p)
+        {
+          hideStart = seq.getLength();
+        }
+        // update visible boundary for sequence
+        if (p < hideStart)
+        {
+          if (!foundStart)
+          {
+            fpos = spos;
+            start = p;
+            foundStart = true;
+          }
+          lastvispos = p;
+          lpos = spos;
+        }
+        // look for next sequence position
+        spos++;
+      }
+    }
+    if (foundStart)
+    {
+      return new int[] { findColumnPosition(start),
+          findColumnPosition(lastvispos), fpos, lpos, firstP, lastP };
+    }
+    // otherwise, sequence was completely hidden
+    return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
+  }
+
+  /**
    * delete any columns in alignmentAnnotation that are hidden (including
    * sequence associated annotation).
    * 
@@ -1191,7 +1329,7 @@ public class ColumnSelection
       {
         if (hiddenColumns != null && isVisible(col.intValue()))
         {
-          selected.add(col);
+          selection.add(col);
         }
       }
     }
@@ -1205,8 +1343,8 @@ public class ColumnSelection
    */
   public void setElementsFrom(ColumnSelection colsel)
   {
-    selected = new IntList();
-    if (colsel.selected != null && colsel.selected.size() > 0)
+    selection = new IntList();
+    if (colsel.selection != null && colsel.selection.size() > 0)
     {
       if (hiddenColumns != null && hiddenColumns.size() > 0)
       {
@@ -1373,7 +1511,7 @@ public class ColumnSelection
    */
   public boolean hasSelectedColumns()
   {
-    return (selected != null && selected.size() > 0);
+    return (selection != null && selection.size() > 0);
   }
 
   /**
@@ -1412,6 +1550,8 @@ public class ColumnSelection
   public boolean filterAnnotations(Annotation[] annotations,
           AnnotationFilterParameter filterParams)
   {
+    // JBPNote - this method needs to be refactored to become independent of
+    // viewmodel package
     this.revealAllHiddenColumns();
     this.clear();
     int count = 0;
@@ -1494,8 +1634,148 @@ public class ColumnSelection
     return false;
   }
 
-  public boolean isSelected(int column)
+  /**
+   * Returns a hashCode built from selected columns and hidden column ranges
+   */
+  @Override
+  public int hashCode()
+  {
+    int hashCode = selection.hashCode();
+    if (hiddenColumns != null)
+    {
+      for (int[] hidden : hiddenColumns)
+      {
+        hashCode = 31 * hashCode + hidden[0];
+        hashCode = 31 * hashCode + hidden[1];
+      }
+    }
+    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)
   {
-    return selected.isSelected(column);
+    if (!(obj instanceof ColumnSelection))
+    {
+      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;
+  }
+
 }