X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FShiftList.java;h=9fb5eca45b35d37e8af48f8386b3bd86da9162fe;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=8885e2c9607706b8b2e9816a4c88fd1769a39382;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index 8885e2c..9fb5eca 100644
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -1,34 +1,33 @@
 /*
- * 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, 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.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 +35,25 @@ 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 +63,9 @@ public class ShiftList
 
   /**
    * shift
-   *
-   * @param pos int
+   * 
+   * @param pos
+   *          int
    * @return int shifted position
    */
   public int shift(int pos)
@@ -75,8 +78,7 @@ 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 +95,7 @@ public class ShiftList
 
   /**
    * invert the shifts
+   * 
    * @return ShiftList with inverse shift operations
    */
   public ShiftList getInverse()
@@ -106,7 +109,7 @@ public class ShiftList
         if (sh != null)
         {
           inverse.shifts.addElement(new int[]
-                                    {sh[0], -sh[1]});
+          { sh[0], -sh[1] });
         }
       }
     }
@@ -114,8 +117,9 @@ 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
    */