X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=5c1707fb9b79b910b1b82fe63377de4914acaf74;hb=4e892da7333869ad8b26d75b25f2c87352ca8c7e;hp=6ef179905a6619bd85644bf000172663850bbec3;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 6ef1799..5c1707f 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -29,13 +29,14 @@ public class ColumnSelection
 {
   Vector selected = new Vector();
 
-  //Vector of int [] {startCol, endCol}
+  // Vector of int [] {startCol, endCol}
   Vector hiddenColumns;
 
   /**
    * Add a column to the selection
-   *
-   * @param col index of column
+   * 
+   * @param col
+   *          index of column
    */
   public void addElement(int col)
   {
@@ -56,8 +57,9 @@ public class ColumnSelection
 
   /**
    * removes col from selection
-   *
-   * @param col index of column to be removed
+   * 
+   * @param col
+   *          index of column to be removed
    */
   public void removeElement(int col)
   {
@@ -71,8 +73,11 @@ public class ColumnSelection
 
   /**
    * removes a range of columns from the selection
-   * @param start int - first column in range to be removed
-   * @param end int - last col
+   * 
+   * @param start
+   *          int - first column in range to be removed
+   * @param end
+   *          int - last col
    */
   public void removeElements(int start, int end)
   {
@@ -88,7 +93,7 @@ public class ColumnSelection
   }
 
   /**
-   *
+   * 
    * @return Vector containing selected columns as Integers
    */
   public Vector getSelected()
@@ -97,9 +102,10 @@ public class ColumnSelection
   }
 
   /**
-   *
-   * @param col index to search for in column selection
-   *
+   * 
+   * @param col
+   *          index to search for in column selection
+   * 
    * @return true if Integer(col) is in selection.
    */
   public boolean contains(int col)
@@ -108,20 +114,21 @@ public class ColumnSelection
   }
 
   /**
-   * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+   * Column number at position i in selection
+   * 
+   * @param i
+   *          index into selected columns
+   * 
+   * @return column number in alignment
    */
   public int columnAt(int i)
   {
-    return ( (Integer) selected.elementAt(i)).intValue();
+    return ((Integer) selected.elementAt(i)).intValue();
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int size()
@@ -130,9 +137,9 @@ public class ColumnSelection
   }
 
   /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+   * rightmost selected column
+   * 
+   * @return rightmost column in alignment that is selected
    */
   public int getMax()
   {
@@ -150,9 +157,9 @@ public class ColumnSelection
   }
 
   /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+   * Leftmost column in selection
+   * 
+   * @return column index of leftmost column in selection
    */
   public int getMin()
   {
@@ -171,9 +178,11 @@ public class ColumnSelection
 
   /**
    * propagate shift in alignment columns to column selection
-   *
-   * @param start beginning of edit
-   * @param left shift in edit (+ve for removal, or -ve for inserts)
+   * 
+   * @param start
+   *          beginning of edit
+   * @param left
+   *          shift in edit (+ve for removal, or -ve for inserts)
    */
   public Vector compensateForEdit(int start, int change)
   {
@@ -197,8 +206,7 @@ public class ColumnSelection
         int[] region = (int[]) hiddenColumns.elementAt(i);
         if (region[0] > start && start + change > region[1])
         {
-          deletedHiddenColumns.addElement(
-              hiddenColumns.elementAt(i));
+          deletedHiddenColumns.addElement(hiddenColumns.elementAt(i));
 
           hiddenColumns.removeElementAt(i);
           i--;
@@ -226,10 +234,13 @@ public class ColumnSelection
   }
 
   /**
-   * propagate shift in alignment columns to column selection
-   * special version of compensateForEdit - allowing for edits within hidden regions
-   * @param start beginning of edit
-   * @param left shift in edit (+ve for removal, or -ve for inserts)
+   * propagate shift in alignment columns to column selection special version of
+   * compensateForEdit - allowing for edits within hidden regions
+   * 
+   * @param start
+   *          beginning of edit
+   * @param left
+   *          shift in edit (+ve for removal, or -ve for inserts)
    */
   private void compensateForDelEdits(int start, int change)
   {
@@ -274,8 +285,9 @@ public class ColumnSelection
   }
 
   /**
-   * Adjust hidden column boundaries based on a series of column
-   * additions or deletions in visible regions.
+   * Adjust hidden column boundaries based on a series of column additions or
+   * deletions in visible regions.
+   * 
    * @param shiftrecord
    * @return
    */
@@ -290,7 +302,7 @@ public class ColumnSelection
         for (int i = 0, j = shifts.size(); i < j; i++)
         {
           int[] sh = (int[]) shifts.elementAt(i);
-          //compensateForEdit(shifted+sh[0], sh[1]);
+          // compensateForEdit(shifted+sh[0], sh[1]);
           compensateForDelEdits(shifted + sh[0], sh[1]);
           shifted -= sh[1];
         }
@@ -301,8 +313,9 @@ public class ColumnSelection
   }
 
   /**
-   * removes intersection of position,length ranges in deletions
-   * from the start,end regions marked in intervals.
+   * removes intersection of position,length ranges in deletions from the
+   * start,end regions marked in intervals.
+   * 
    * @param deletions
    * @param intervals
    * @return
@@ -389,7 +402,8 @@ public class ColumnSelection
         }
       }
     }
-    return pruned; // true if any interval was removed or modified by operations.
+    return pruned; // true if any interval was removed or modified by
+    // operations.
   }
 
   private boolean pruneColumnList(Vector deletion, Vector list)
@@ -400,7 +414,7 @@ public class ColumnSelection
     int i = 0, j = list.size();
     while (i < j && s <= t)
     {
-      int c = ( (Integer) list.elementAt(i++)).intValue();
+      int c = ((Integer) list.elementAt(i++)).intValue();
       if (sr[0] <= c)
       {
         if (sr[1] + sr[0] >= c)
@@ -422,8 +436,9 @@ public class ColumnSelection
   }
 
   /**
-   * remove any hiddenColumns or selected columns and shift remaining
-   * based on a series of position, range deletions.
+   * remove any hiddenColumns or selected columns and shift remaining based on a
+   * series of position, range deletions.
+   * 
    * @param deletions
    */
   public void pruneDeletions(ShiftList deletions)
@@ -457,9 +472,11 @@ public class ColumnSelection
   }
 
   /**
-   * This Method is used to return all the HiddenColumn regions
-   * less than the given index.
-   * @param end int
+   * This Method is used to return all the HiddenColumn regions less than the
+   * given index.
+   * 
+   * @param end
+   *          int
    * @return Vector
    */
   public Vector getHiddenColumns()
@@ -469,7 +486,9 @@ public class ColumnSelection
 
   /**
    * Return absolute column index for a visible column index
-   * @param column int column index in alignment view
+   * 
+   * @param column
+   *          int column index in alignment view
    * @return alignment column index for column
    */
   public int adjustForHiddenColumns(int column)
@@ -490,9 +509,11 @@ public class ColumnSelection
   }
 
   /**
-   * Use this method to find out where a visible column is in the alignment
-   * when hidden columns exist
-   * @param hiddenColumn int
+   * Use this method to find out where a visible column is in the alignment when
+   * hidden columns exist
+   * 
+   * @param hiddenColumn
+   *          int
    * @return int
    */
   public int findColumnPosition(int hiddenColumn)
@@ -510,8 +531,7 @@ public class ColumnSelection
           result -= region[1] + 1 - region[0];
         }
         index++;
-      }
-      while (index < hiddenColumns.size());
+      } while (index < hiddenColumns.size());
 
       result -= gaps;
     }
@@ -540,8 +560,7 @@ public class ColumnSelection
         gaps += region[1] + 1 - region[0];
         result = region[1] + 1;
         index++;
-      }
-      while (index < hiddenRegion + 1);
+      } while (index < hiddenRegion + 1);
 
       result -= gaps;
     }
@@ -550,10 +569,11 @@ public class ColumnSelection
   }
 
   /**
-   * THis method returns the rightmost limit of a
-   * region of an alignment with hidden columns.
-   * In otherwords, the next hidden column.
-   * @param index int
+   * THis method returns the rightmost limit of a region of an alignment with
+   * hidden columns. In otherwords, the next hidden column.
+   * 
+   * @param index
+   *          int
    */
   public int getHiddenBoundaryRight(int alPos)
   {
@@ -569,8 +589,7 @@ public class ColumnSelection
         }
 
         index++;
-      }
-      while (index < hiddenColumns.size());
+      } while (index < hiddenColumns.size());
     }
 
     return alPos;
@@ -578,10 +597,11 @@ public class ColumnSelection
   }
 
   /**
-   * THis method returns the rightmost limit of a
-   * region of an alignment with hidden columns.
-   * In otherwords, the next hidden column.
-   * @param index int
+   * This method returns the leftmost limit of a region of an alignment with
+   * hidden columns. In otherwords, the previous hidden column.
+   * 
+   * @param index
+   *          int
    */
   public int getHiddenBoundaryLeft(int alPos)
   {
@@ -597,8 +617,7 @@ public class ColumnSelection
         }
 
         index--;
-      }
-      while (index > -1);
+      } while (index > -1);
     }
 
     return alPos;
@@ -609,7 +628,7 @@ public class ColumnSelection
   {
     while (size() > 0)
     {
-      int column = ( (Integer) getSelected().firstElement()).intValue();
+      int column = ((Integer) getSelected().firstElement()).intValue();
       hideColumns(column);
     }
 
@@ -637,7 +656,7 @@ public class ColumnSelection
       else if (end < region[0] && start < region[0])
       {
         hiddenColumns.insertElementAt(new int[]
-                                      {start, end}, i);
+        { start, end }, i);
         added = true;
         break;
       }
@@ -650,15 +669,17 @@ public class ColumnSelection
     else if (!added)
     {
       hiddenColumns.addElement(new int[]
-                               {start, end});
+      { start, end });
     }
 
   }
 
   /**
-   * This method will find a range of selected columns
-   * around the column specified
-   * @param res int
+   * This method will find a range of selected columns around the column
+   * specified
+   * 
+   * @param res
+   *          int
    */
   public void hideColumns(int col)
   {
@@ -727,19 +748,22 @@ public class ColumnSelection
 
   public boolean isVisible(int column)
   {
-    for (int i = 0; i < hiddenColumns.size(); i++)
-    {
-      int[] region = (int[]) hiddenColumns.elementAt(i);
-      if (column >= region[0] && column <= region[1])
+    if (hiddenColumns != null)
+      for (int i = 0; i < hiddenColumns.size(); i++)
       {
-        return false;
+        int[] region = (int[]) hiddenColumns.elementAt(i);
+        if (column >= region[0] && column <= region[1])
+        {
+          return false;
+        }
       }
-    }
+
     return true;
   }
 
   /**
    * Copy constructor
+   * 
    * @param copy
    */
   public ColumnSelection(ColumnSelection copy)
@@ -780,7 +804,7 @@ public class ColumnSelection
   }
 
   public String[] getVisibleSequenceStrings(int start, int end,
-                                            SequenceI[] seqs)
+          SequenceI[] seqs)
   {
     int i, iSize = seqs.length;
     String selection[] = new String[iSize];
@@ -841,10 +865,13 @@ public class ColumnSelection
 
   /**
    * return all visible segments between the given start and end boundaries
-   *
-   * @param start (first column inclusive from 0)
-   * @param end (last column - not inclusive)
-   * @return int[] {i_start, i_end, ..} where intervals lie in start<=i_start<=i_end<end
+   * 
+   * @param start
+   *          (first column inclusive from 0)
+   * @param end
+   *          (last column - not inclusive)
+   * @return int[] {i_start, i_end, ..} where intervals lie in
+   *         start<=i_start<=i_end<end
    */
   public int[] getVisibleContigs(int start, int end)
   {
@@ -870,7 +897,7 @@ public class ColumnSelection
         if (hideStart > vstart)
         {
           visiblecontigs.addElement(new int[]
-                                    {vstart, hideStart - 1});
+          { vstart, hideStart - 1 });
         }
         vstart = hideEnd + 1;
       }
@@ -878,7 +905,7 @@ public class ColumnSelection
       if (vstart < end)
       {
         visiblecontigs.addElement(new int[]
-                                  {vstart, end - 1});
+        { vstart, end - 1 });
       }
       int[] vcontigs = new int[visiblecontigs.size() * 2];
       for (int i = 0, j = visiblecontigs.size(); i < j; i++)
@@ -894,8 +921,187 @@ public class ColumnSelection
     else
     {
       return new int[]
+      { start, end - 1 };
+    }
+  }
+
+  /**
+   * delete any columns in alignmentAnnotation that are hidden (including
+   * sequence associated annotation).
+   * 
+   * @param alignmentAnnotation
+   */
+  public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
+  {
+    makeVisibleAnnotation(-1, -1, alignmentAnnotation);
+  }
+
+  /**
+   * delete any columns in alignmentAnnotation that are hidden (including
+   * sequence associated annotation).
+   * 
+   * @param start
+   *          remove any annotation to the right of this column
+   * @param end
+   *          remove any annotation to the left of this column
+   * @param alignmentAnnotation
+   *          the annotation to operate on
+   */
+  public void makeVisibleAnnotation(int start, int end,
+          AlignmentAnnotation alignmentAnnotation)
+  {
+    if (alignmentAnnotation.annotations == null)
+    {
+      return;
+    }
+    if (start == end && end == -1)
+    {
+      start = 0;
+      end = alignmentAnnotation.annotations.length;
+    }
+    if (hiddenColumns != null && hiddenColumns.size() > 0)
+    {
+      // then mangle the alignmentAnnotation annotation array
+      Vector annels = new Vector();
+      Annotation[] els = null;
+      Vector regions = getHiddenColumns();
+      int blockStart = start, blockEnd = end;
+      int[] region;
+      int hideStart, hideEnd, w = 0;
+
+      for (int j = 0; j < regions.size(); j++)
+      {
+        region = (int[]) regions.elementAt(j);
+        hideStart = region[0];
+        hideEnd = region[1];
+
+        if (hideStart < start)
+        {
+          continue;
+        }
+
+        blockStart = Math.min(blockStart, hideEnd + 1);
+        blockEnd = Math.min(blockEnd, hideStart);
+
+        if (blockStart > blockEnd)
+        {
+          break;
+        }
+
+        annels.addElement(els = new Annotation[blockEnd - blockStart]);
+        System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
+                0, els.length);
+        w += els.length;
+        blockStart = hideEnd + 1;
+        blockEnd = end;
+      }
+
+      if (end > blockStart)
+      {
+        annels.addElement(els = new Annotation[end - blockStart + 1]);
+        if ((els.length + blockStart) <= alignmentAnnotation.annotations.length)
+        {
+          // copy just the visible segment of the annotation row
+          System.arraycopy(alignmentAnnotation.annotations, blockStart,
+                  els, 0, els.length);
+        }
+        else
+        {
+          // copy to the end of the annotation row
+          System.arraycopy(alignmentAnnotation.annotations, blockStart,
+                  els, 0,
+                  (alignmentAnnotation.annotations.length - blockStart));
+        }
+        w += els.length;
+      }
+      if (w == 0)
+        return;
+      Enumeration e = annels.elements();
+      alignmentAnnotation.annotations = new Annotation[w];
+      w = 0;
+      while (e.hasMoreElements())
+      {
+        Annotation[] chnk = (Annotation[]) e.nextElement();
+        System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
+                chnk.length);
+        w += chnk.length;
+      }
+    }
+    else
+    {
+      alignmentAnnotation.restrict(start, end);
+    }
+  }
+
+  /**
+   * Invert the column selection from first to end-1. leaves hiddenColumns
+   * untouched (and unselected)
+   * 
+   * @param first
+   * @param end
+   */
+  public void invertColumnSelection(int first, int width)
+  {
+    boolean hasHidden = hiddenColumns != null && hiddenColumns.size() > 0;
+    for (int i = first; i < width; i++)
+    {
+      if (contains(i))
+      {
+        removeElement(i);
+      }
+      else
+      {
+        if (!hasHidden || isVisible(i))
+        {
+          addElement(i);
+        }
+      }
+    }
+  }
+
+  /**
+   * add in any unselected columns from the given column selection, excluding any that are hidden.
+   * @param colsel
+   */
+  public void addElementsFrom(ColumnSelection colsel)
+  {
+    if (colsel != null && colsel.size() > 0)
+    {
+      Enumeration e = colsel.getSelected().elements();
+      while (e.hasMoreElements())
+      {
+        Object eo = e.nextElement();
+        if (hiddenColumns!=null && isVisible(((Integer) eo).intValue())) {
+          if (!selected.contains(eo))
           {
-          start, end - 1};
+            selected.addElement(eo);
+          }
+        }
+      }
+    }
+  }
+/**
+ * set the selected columns the given column selection, excluding any columns that are hidden. 
+ * @param colsel
+ */
+  public void setElementsFrom(ColumnSelection colsel)
+  {
+    selected = new Vector();
+    if (colsel.selected != null && colsel.selected.size() > 0)
+    {
+      if (hiddenColumns!=null && hiddenColumns.size()>0)
+      {
+        // only select visible columns in this columns selection
+        selected = new Vector();
+        addElementsFrom(colsel);
+      } else {
+        // add everything regardless
+        Enumeration en = colsel.selected.elements();
+        while (en.hasMoreElements())
+        {
+          selected.addElement(en.nextElement());
+        }
+      }
     }
   }
 }