X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FShiftList.java;h=be416dcc6e144e3e277ae6ca05cfb928fd55f480;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=8885e2c9607706b8b2e9816a4c88fd1769a39382;hpb=60f2d6c034560415fd0139c8bc7df0c19cae1186;p=jalview.git

diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index 8885e2c..be416dc 100644
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.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 (Version 2.4)
+ * Copyright (C) 2008 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
@@ -21,14 +21,14 @@ package jalview.util;
 import java.util.*;
 
 /**
- * ShiftList
- * Simple way of mapping a linear series to a new linear range with new points introduced.
- * Use at your own risk!
- * Now growing to be used for interval ranges (position, offset) storing deletions/insertions
+ * ShiftList Simple way of mapping a linear series to a new linear range with
+ * new points introduced. Use at your own risk! Now growing to be used for
+ * interval ranges (position, offset) storing deletions/insertions
  */
 public class ShiftList
 {
   public Vector shifts;
+
   public ShiftList()
   {
     shifts = new Vector();
@@ -36,22 +36,25 @@ public class ShiftList
 
   /**
    * addShift
-   * @param pos start position for shift (in original reference frame)
-   * @param shift length of shift
+   * 
+   * @param pos
+   *                start position for shift (in original reference frame)
+   * @param shift
+   *                length of shift
    */
   public void addShift(int pos, int shift)
   {
     int sidx = 0;
     int[] rshift = null;
-    while (sidx < shifts.size() &&
-           (rshift = (int[]) shifts.elementAt(sidx))[0] < pos)
+    while (sidx < shifts.size()
+            && (rshift = (int[]) shifts.elementAt(sidx))[0] < pos)
     {
       sidx++;
     }
     if (sidx == shifts.size())
     {
       shifts.insertElementAt(new int[]
-                             {pos, shift}, sidx);
+      { pos, shift }, sidx);
     }
     else
     {
@@ -61,8 +64,9 @@ public class ShiftList
 
   /**
    * shift
-   *
-   * @param pos int
+   * 
+   * @param pos
+   *                int
    * @return int shifted position
    */
   public int shift(int pos)
@@ -75,8 +79,7 @@ public class ShiftList
     int sidx = 0;
     int rshift[];
     while (sidx < shifts.size()
-           &&
-           (rshift = ( (int[]) shifts.elementAt(sidx++)))[0] <= pos)
+            && (rshift = ((int[]) shifts.elementAt(sidx++)))[0] <= pos)
     {
       shifted += rshift[1];
     }
@@ -93,6 +96,7 @@ public class ShiftList
 
   /**
    * invert the shifts
+   * 
    * @return ShiftList with inverse shift operations
    */
   public ShiftList getInverse()
@@ -106,7 +110,7 @@ public class ShiftList
         if (sh != null)
         {
           inverse.shifts.addElement(new int[]
-                                    {sh[0], -sh[1]});
+          { sh[0], -sh[1] });
         }
       }
     }
@@ -114,8 +118,9 @@ public class ShiftList
   }
 
   /**
-   * parse a 1d map of position 1<i<n to L<pos[i]<N
-   * such as that returned from SequenceI.gapMap()
+   * parse a 1d map of position 1<i<n to L<pos[i]<N such as that returned
+   * from SequenceI.gapMap()
+   * 
    * @param gapMap
    * @return shifts from map index to mapped position
    */