X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=d0fc9277f5c5bbda923b5b7f0acc4d695c5f11de;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=4904495ee9ad8b919fecee944b3a8668900b6148;hpb=a706a0f1f86af677c05c12713e791b78320003e6;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 4904495..d0fc927 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.datamodel;
 
@@ -29,13 +28,14 @@ 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 +56,9 @@ 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 +72,11 @@ 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 +92,7 @@ public class ColumnSelection
   }
 
   /**
-   *
+   * 
    * @return Vector containing selected columns as Integers
    */
   public Vector getSelected()
@@ -97,9 +101,10 @@ 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 +113,21 @@ 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 +136,9 @@ public class ColumnSelection
   }
 
   /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+   * rightmost selected column
+   * 
+   * @return rightmost column in alignment that is selected
    */
   public int getMax()
   {
@@ -150,9 +156,9 @@ 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 +177,11 @@ 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 +205,7 @@ 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 +233,13 @@ 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 +284,9 @@ 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 +301,7 @@ 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 +312,9 @@ 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 +401,8 @@ 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 +413,7 @@ 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 +435,9 @@ 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 +471,11 @@ 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 +485,9 @@ 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 +508,12 @@ 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 column will appear in the visible
+   * alignment when hidden columns exist. If the column is not visible, then the
+   * left-most visible column will always be returned.
+   * 
+   * @param hiddenColumn
+   *          int
    * @return int
    */
   public int findColumnPosition(int hiddenColumn)
@@ -501,22 +522,21 @@ public class ColumnSelection
     if (hiddenColumns != null)
     {
       int index = 0;
-      int gaps = 0;
+      int[] region;
       do
       {
-        int[] region = (int[]) hiddenColumns.elementAt(index);
+        region = (int[]) hiddenColumns.elementAt(index++);
         if (hiddenColumn > region[1])
         {
           result -= region[1] + 1 - region[0];
         }
-        index++;
+      } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
+      if (hiddenColumn > region[0] && hiddenColumn < region[1])
+      {
+        return region[0] + hiddenColumn - result;
       }
-      while (index < hiddenColumns.size());
-
-      result -= gaps;
     }
-
-    return result;
+    return result; // return the shifted position after removing hidden columns.
   }
 
   /**
@@ -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 leftmost limit of a
-   * region of an alignment with hidden columns.
-   * In otherwords, the previous 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)
   {
@@ -742,6 +763,7 @@ public class ColumnSelection
 
   /**
    * Copy constructor
+   * 
    * @param copy
    */
   public ColumnSelection(ColumnSelection copy)
@@ -782,7 +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];
@@ -843,10 +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)
   {
@@ -872,7 +897,7 @@ public class ColumnSelection
         if (hideStart > vstart)
         {
           visiblecontigs.addElement(new int[]
-                                    {vstart, hideStart - 1});
+          { vstart, hideStart - 1 });
         }
         vstart = hideEnd + 1;
       }
@@ -880,7 +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++)
@@ -896,8 +921,325 @@ 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))
+          {
+            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());
+        }
+      }
+    }
+  }
+
+  /**
+   * Add gaps into the sequences aligned to profileseq under the given
+   * AlignmentView
+   * 
+   * @param profileseq
+   * @param al - alignment to have gaps inserted into it
+   * @param input - alignment view where sequence corresponding to profileseq is first entry
+   * @return new Column selection for new alignment view, with insertions into profileseq marked as hidden.
+   */
+  public static ColumnSelection propagateInsertions(SequenceI profileseq,
+          Alignment al, AlignmentView input)
+  {
+    int profsqpos=0;
+    
+//    return propagateInsertions(profileseq, al, )
+    char gc = al.getGapCharacter();
+    Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);
+    ColumnSelection nview = (ColumnSelection) alandcolsel[1];
+    SequenceI origseq = ((SequenceI[]) alandcolsel[0])[profsqpos];
+    nview.propagateInsertions(profileseq,
+            al, origseq);
+    return nview;
+  }
+  /**
+   * 
+   * @param profileseq - sequence in al which corresponds to origseq 
+   * @param al - alignment which is to have gaps inserted into it
+   * @param origseq - sequence corresponding to profileseq which defines gap map for modifying al
+   */
+  public void propagateInsertions(SequenceI profileseq, AlignmentI al, SequenceI origseq)
+  {
+    char gc = al.getGapCharacter();
+    // recover mapping between sequence's non-gap positions and positions 
+    // mapping to view.
+    pruneDeletions(ShiftList
+            .parseMap(origseq
+                    .gapMap())); 
+    int[] viscontigs = getVisibleContigs(0, profileseq.getLength());
+    int spos = 0;
+    int offset = 0;
+    // input.pruneDeletions(ShiftList.parseMap(((SequenceI[])
+    // alandcolsel[0])[0].gapMap()))
+    // add profile to visible contigs
+    for (int v = 0; v < viscontigs.length; v += 2)
+    {
+      if (viscontigs[v] > spos)
+      {
+        StringBuffer sb = new StringBuffer();
+        for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
+        {
+          sb.append(gc);
+        }
+        for (int s = 0, ns = al.getHeight(); s < ns; s++)
+        {
+          SequenceI sqobj = al.getSequenceAt(s);
+          if (sqobj != profileseq)
           {
-          start, end - 1};
+            String sq = al.getSequenceAt(s).getSequenceAsString();
+            if (sq.length() <= spos + offset)
+            {
+              // pad sequence
+              int diff = spos + offset - sq.length() - 1;
+              if (diff > 0)
+              {
+                // pad gaps
+                sq = sq + sb;
+                while ((diff = spos + offset - sq.length() - 1) > 0)
+                {
+                  //sq = sq
+                  //        + ((diff >= sb.length()) ? sb.toString() : sb
+                  //                .substring(0, diff));
+                  if (diff>=sb.length()) {
+                    sq+=sb.toString();
+                  } else {
+                    char[] buf = new char[diff];
+                    sb.getChars(0, diff, buf, 0);
+                    sq+=buf.toString();
+                  }
+                }
+              }
+              sq += sb.toString();
+            }
+            else
+            {
+              al.getSequenceAt(s).setSequence(
+                      sq.substring(0, spos + offset) + sb.toString()
+                              + sq.substring(spos + offset));
+            }
+          }
+        }
+        // offset+=sb.length();
+      }
+      spos = viscontigs[v + 1] + 1;
+    }
+    if ((offset + spos) < profileseq.getLength())
+    {
+      // pad the final region with gaps.
+      StringBuffer sb = new StringBuffer();
+      for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
+      {
+        sb.append(gc);
+      }
+      for (int s = 0, ns = al.getHeight(); s < ns; s++)
+      {
+        SequenceI sqobj = al.getSequenceAt(s);
+        if (sqobj==profileseq)
+        {
+          continue;
+        }
+        String sq = sqobj.getSequenceAsString();
+        // pad sequence
+        int diff = origseq.getLength() - sq.length();
+        while (diff > 0)
+        {
+          //sq = sq
+          //        + ((diff >= sb.length()) ? sb.toString() : sb
+          //                .substring(0, diff));
+          if (diff>=sb.length()) {
+            sq+=sb.toString();
+          } else {
+            char[] buf = new char[diff];
+            sb.getChars(0, diff, buf, 0);
+            sq+=buf.toString();
+          }
+          diff = origseq.getLength() - sq.length();
+        }
+      }
     }
   }
 }